diff test-data/results/intersected_vcf.vcf @ 1:2c7bcc1219fc draft

Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL.
author galaxyp
date Thu, 16 Aug 2018 12:27:35 -0400
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/results/intersected_vcf.vcf	Thu Aug 16 12:27:35 2018 -0400
@@ -0,0 +1,516 @@
+##fileformat=VCFv4.2
+##fileDate=20180518
+##source=freeBayes  v1.1.0-46-g8d2b3a0-dirty
+##reference=/panfs/roc/rissdb/galaxy/genomes/hg38/seq/hg38.fa
+##contig=<ID=chr1,length=248956422>
+##contig=<ID=chr10,length=133797422>
+##contig=<ID=chr11,length=135086622>
+##contig=<ID=chr11_KI270721v1_random,length=100316>
+##contig=<ID=chr12,length=133275309>
+##contig=<ID=chr13,length=114364328>
+##contig=<ID=chr14,length=107043718>
+##contig=<ID=chr14_GL000009v2_random,length=201709>
+##contig=<ID=chr14_GL000225v1_random,length=211173>
+##contig=<ID=chr14_KI270722v1_random,length=194050>
+##contig=<ID=chr14_GL000194v1_random,length=191469>
+##contig=<ID=chr14_KI270723v1_random,length=38115>
+##contig=<ID=chr14_KI270724v1_random,length=39555>
+##contig=<ID=chr14_KI270725v1_random,length=172810>
+##contig=<ID=chr14_KI270726v1_random,length=43739>
+##contig=<ID=chr15,length=101991189>
+##contig=<ID=chr15_KI270727v1_random,length=448248>
+##contig=<ID=chr16,length=90338345>
+##contig=<ID=chr16_KI270728v1_random,length=1872759>
+##contig=<ID=chr17,length=83257441>
+##contig=<ID=chr17_GL000205v2_random,length=185591>
+##contig=<ID=chr17_KI270729v1_random,length=280839>
+##contig=<ID=chr17_KI270730v1_random,length=112551>
+##contig=<ID=chr18,length=80373285>
+##contig=<ID=chr19,length=58617616>
+##contig=<ID=chr1_KI270706v1_random,length=175055>
+##contig=<ID=chr1_KI270707v1_random,length=32032>
+##contig=<ID=chr1_KI270708v1_random,length=127682>
+##contig=<ID=chr1_KI270709v1_random,length=66860>
+##contig=<ID=chr1_KI270710v1_random,length=40176>
+##contig=<ID=chr1_KI270711v1_random,length=42210>
+##contig=<ID=chr1_KI270712v1_random,length=176043>
+##contig=<ID=chr1_KI270713v1_random,length=40745>
+##contig=<ID=chr1_KI270714v1_random,length=41717>
+##contig=<ID=chr2,length=242193529>
+##contig=<ID=chr20,length=64444167>
+##contig=<ID=chr21,length=46709983>
+##contig=<ID=chr22,length=50818468>
+##contig=<ID=chr22_KI270731v1_random,length=150754>
+##contig=<ID=chr22_KI270732v1_random,length=41543>
+##contig=<ID=chr22_KI270733v1_random,length=179772>
+##contig=<ID=chr22_KI270734v1_random,length=165050>
+##contig=<ID=chr22_KI270735v1_random,length=42811>
+##contig=<ID=chr22_KI270736v1_random,length=181920>
+##contig=<ID=chr22_KI270737v1_random,length=103838>
+##contig=<ID=chr22_KI270738v1_random,length=99375>
+##contig=<ID=chr22_KI270739v1_random,length=73985>
+##contig=<ID=chr2_KI270715v1_random,length=161471>
+##contig=<ID=chr2_KI270716v1_random,length=153799>
+##contig=<ID=chr3,length=198295559>
+##contig=<ID=chr3_GL000221v1_random,length=155397>
+##contig=<ID=chr4,length=190214555>
+##contig=<ID=chr4_GL000008v2_random,length=209709>
+##contig=<ID=chr5,length=181538259>
+##contig=<ID=chr5_GL000208v1_random,length=92689>
+##contig=<ID=chr6,length=170805979>
+##contig=<ID=chr7,length=159345973>
+##contig=<ID=chr8,length=145138636>
+##contig=<ID=chr9,length=138394717>
+##contig=<ID=chr9_KI270717v1_random,length=40062>
+##contig=<ID=chr9_KI270718v1_random,length=38054>
+##contig=<ID=chr9_KI270719v1_random,length=176845>
+##contig=<ID=chr9_KI270720v1_random,length=39050>
+##contig=<ID=chr1_KI270762v1_alt,length=354444>
+##contig=<ID=chr1_KI270766v1_alt,length=256271>
+##contig=<ID=chr1_KI270760v1_alt,length=109528>
+##contig=<ID=chr1_KI270765v1_alt,length=185285>
+##contig=<ID=chr1_GL383518v1_alt,length=182439>
+##contig=<ID=chr1_GL383519v1_alt,length=110268>
+##contig=<ID=chr1_GL383520v2_alt,length=366580>
+##contig=<ID=chr1_KI270764v1_alt,length=50258>
+##contig=<ID=chr1_KI270763v1_alt,length=911658>
+##contig=<ID=chr1_KI270759v1_alt,length=425601>
+##contig=<ID=chr1_KI270761v1_alt,length=165834>
+##contig=<ID=chr2_KI270770v1_alt,length=136240>
+##contig=<ID=chr2_KI270773v1_alt,length=70887>
+##contig=<ID=chr2_KI270774v1_alt,length=223625>
+##contig=<ID=chr2_KI270769v1_alt,length=120616>
+##contig=<ID=chr2_GL383521v1_alt,length=143390>
+##contig=<ID=chr2_KI270772v1_alt,length=133041>
+##contig=<ID=chr2_KI270775v1_alt,length=138019>
+##contig=<ID=chr2_KI270771v1_alt,length=110395>
+##contig=<ID=chr2_KI270768v1_alt,length=110099>
+##contig=<ID=chr2_GL582966v2_alt,length=96131>
+##contig=<ID=chr2_GL383522v1_alt,length=123821>
+##contig=<ID=chr2_KI270776v1_alt,length=174166>
+##contig=<ID=chr2_KI270767v1_alt,length=161578>
+##contig=<ID=chr3_JH636055v2_alt,length=173151>
+##contig=<ID=chr3_KI270783v1_alt,length=109187>
+##contig=<ID=chr3_KI270780v1_alt,length=224108>
+##contig=<ID=chr3_GL383526v1_alt,length=180671>
+##contig=<ID=chr3_KI270777v1_alt,length=173649>
+##contig=<ID=chr3_KI270778v1_alt,length=248252>
+##contig=<ID=chr3_KI270781v1_alt,length=113034>
+##contig=<ID=chr3_KI270779v1_alt,length=205312>
+##contig=<ID=chr3_KI270782v1_alt,length=162429>
+##contig=<ID=chr3_KI270784v1_alt,length=184404>
+##contig=<ID=chr4_KI270790v1_alt,length=220246>
+##contig=<ID=chr4_GL383528v1_alt,length=376187>
+##contig=<ID=chr4_KI270787v1_alt,length=111943>
+##contig=<ID=chr4_GL000257v2_alt,length=586476>
+##contig=<ID=chr4_KI270788v1_alt,length=158965>
+##contig=<ID=chr4_GL383527v1_alt,length=164536>
+##contig=<ID=chr4_KI270785v1_alt,length=119912>
+##contig=<ID=chr4_KI270789v1_alt,length=205944>
+##contig=<ID=chr4_KI270786v1_alt,length=244096>
+##contig=<ID=chr5_KI270793v1_alt,length=126136>
+##contig=<ID=chr5_KI270792v1_alt,length=179043>
+##contig=<ID=chr5_KI270791v1_alt,length=195710>
+##contig=<ID=chr5_GL383532v1_alt,length=82728>
+##contig=<ID=chr5_GL949742v1_alt,length=226852>
+##contig=<ID=chr5_KI270794v1_alt,length=164558>
+##contig=<ID=chr5_GL339449v2_alt,length=1612928>
+##contig=<ID=chr5_GL383530v1_alt,length=101241>
+##contig=<ID=chr5_KI270796v1_alt,length=172708>
+##contig=<ID=chr5_GL383531v1_alt,length=173459>
+##contig=<ID=chr5_KI270795v1_alt,length=131892>
+##contig=<ID=chr6_GL000250v2_alt,length=4672374>
+##contig=<ID=chr6_KI270800v1_alt,length=175808>
+##contig=<ID=chr6_KI270799v1_alt,length=152148>
+##contig=<ID=chr6_GL383533v1_alt,length=124736>
+##contig=<ID=chr6_KI270801v1_alt,length=870480>
+##contig=<ID=chr6_KI270802v1_alt,length=75005>
+##contig=<ID=chr6_KB021644v2_alt,length=185823>
+##contig=<ID=chr6_KI270797v1_alt,length=197536>
+##contig=<ID=chr6_KI270798v1_alt,length=271782>
+##contig=<ID=chr7_KI270804v1_alt,length=157952>
+##contig=<ID=chr7_KI270809v1_alt,length=209586>
+##contig=<ID=chr7_KI270806v1_alt,length=158166>
+##contig=<ID=chr7_GL383534v2_alt,length=119183>
+##contig=<ID=chr7_KI270803v1_alt,length=1111570>
+##contig=<ID=chr7_KI270808v1_alt,length=271455>
+##contig=<ID=chr7_KI270807v1_alt,length=126434>
+##contig=<ID=chr7_KI270805v1_alt,length=209988>
+##contig=<ID=chr8_KI270818v1_alt,length=145606>
+##contig=<ID=chr8_KI270812v1_alt,length=282736>
+##contig=<ID=chr8_KI270811v1_alt,length=292436>
+##contig=<ID=chr8_KI270821v1_alt,length=985506>
+##contig=<ID=chr8_KI270813v1_alt,length=300230>
+##contig=<ID=chr8_KI270822v1_alt,length=624492>
+##contig=<ID=chr8_KI270814v1_alt,length=141812>
+##contig=<ID=chr8_KI270810v1_alt,length=374415>
+##contig=<ID=chr8_KI270819v1_alt,length=133535>
+##contig=<ID=chr8_KI270820v1_alt,length=36640>
+##contig=<ID=chr8_KI270817v1_alt,length=158983>
+##contig=<ID=chr8_KI270816v1_alt,length=305841>
+##contig=<ID=chr8_KI270815v1_alt,length=132244>
+##contig=<ID=chr9_GL383539v1_alt,length=162988>
+##contig=<ID=chr9_GL383540v1_alt,length=71551>
+##contig=<ID=chr9_GL383541v1_alt,length=171286>
+##contig=<ID=chr9_GL383542v1_alt,length=60032>
+##contig=<ID=chr9_KI270823v1_alt,length=439082>
+##contig=<ID=chr10_GL383545v1_alt,length=179254>
+##contig=<ID=chr10_KI270824v1_alt,length=181496>
+##contig=<ID=chr10_GL383546v1_alt,length=309802>
+##contig=<ID=chr10_KI270825v1_alt,length=188315>
+##contig=<ID=chr11_KI270832v1_alt,length=210133>
+##contig=<ID=chr11_KI270830v1_alt,length=177092>
+##contig=<ID=chr11_KI270831v1_alt,length=296895>
+##contig=<ID=chr11_KI270829v1_alt,length=204059>
+##contig=<ID=chr11_GL383547v1_alt,length=154407>
+##contig=<ID=chr11_JH159136v1_alt,length=200998>
+##contig=<ID=chr11_JH159137v1_alt,length=191409>
+##contig=<ID=chr11_KI270827v1_alt,length=67707>
+##contig=<ID=chr11_KI270826v1_alt,length=186169>
+##contig=<ID=chr12_GL877875v1_alt,length=167313>
+##contig=<ID=chr12_GL877876v1_alt,length=408271>
+##contig=<ID=chr12_KI270837v1_alt,length=40090>
+##contig=<ID=chr12_GL383549v1_alt,length=120804>
+##contig=<ID=chr12_KI270835v1_alt,length=238139>
+##contig=<ID=chr12_GL383550v2_alt,length=169178>
+##contig=<ID=chr12_GL383552v1_alt,length=138655>
+##contig=<ID=chr12_GL383553v2_alt,length=152874>
+##contig=<ID=chr12_KI270834v1_alt,length=119498>
+##contig=<ID=chr12_GL383551v1_alt,length=184319>
+##contig=<ID=chr12_KI270833v1_alt,length=76061>
+##contig=<ID=chr12_KI270836v1_alt,length=56134>
+##contig=<ID=chr13_KI270840v1_alt,length=191684>
+##contig=<ID=chr13_KI270839v1_alt,length=180306>
+##contig=<ID=chr13_KI270843v1_alt,length=103832>
+##contig=<ID=chr13_KI270841v1_alt,length=169134>
+##contig=<ID=chr13_KI270838v1_alt,length=306913>
+##contig=<ID=chr13_KI270842v1_alt,length=37287>
+##contig=<ID=chr14_KI270844v1_alt,length=322166>
+##contig=<ID=chr14_KI270847v1_alt,length=1511111>
+##contig=<ID=chr14_KI270845v1_alt,length=180703>
+##contig=<ID=chr14_KI270846v1_alt,length=1351393>
+##contig=<ID=chr15_KI270852v1_alt,length=478999>
+##contig=<ID=chr15_KI270851v1_alt,length=263054>
+##contig=<ID=chr15_KI270848v1_alt,length=327382>
+##contig=<ID=chr15_GL383554v1_alt,length=296527>
+##contig=<ID=chr15_KI270849v1_alt,length=244917>
+##contig=<ID=chr15_GL383555v2_alt,length=388773>
+##contig=<ID=chr15_KI270850v1_alt,length=430880>
+##contig=<ID=chr16_KI270854v1_alt,length=134193>
+##contig=<ID=chr16_KI270856v1_alt,length=63982>
+##contig=<ID=chr16_KI270855v1_alt,length=232857>
+##contig=<ID=chr16_KI270853v1_alt,length=2659700>
+##contig=<ID=chr16_GL383556v1_alt,length=192462>
+##contig=<ID=chr16_GL383557v1_alt,length=89672>
+##contig=<ID=chr17_GL383563v3_alt,length=375691>
+##contig=<ID=chr17_KI270862v1_alt,length=391357>
+##contig=<ID=chr17_KI270861v1_alt,length=196688>
+##contig=<ID=chr17_KI270857v1_alt,length=2877074>
+##contig=<ID=chr17_JH159146v1_alt,length=278131>
+##contig=<ID=chr17_JH159147v1_alt,length=70345>
+##contig=<ID=chr17_GL383564v2_alt,length=133151>
+##contig=<ID=chr17_GL000258v2_alt,length=1821992>
+##contig=<ID=chr17_GL383565v1_alt,length=223995>
+##contig=<ID=chr17_KI270858v1_alt,length=235827>
+##contig=<ID=chr17_KI270859v1_alt,length=108763>
+##contig=<ID=chr17_GL383566v1_alt,length=90219>
+##contig=<ID=chr17_KI270860v1_alt,length=178921>
+##contig=<ID=chr18_KI270864v1_alt,length=111737>
+##contig=<ID=chr18_GL383567v1_alt,length=289831>
+##contig=<ID=chr18_GL383570v1_alt,length=164789>
+##contig=<ID=chr18_GL383571v1_alt,length=198278>
+##contig=<ID=chr18_GL383568v1_alt,length=104552>
+##contig=<ID=chr18_GL383569v1_alt,length=167950>
+##contig=<ID=chr18_GL383572v1_alt,length=159547>
+##contig=<ID=chr18_KI270863v1_alt,length=167999>
+##contig=<ID=chr19_KI270868v1_alt,length=61734>
+##contig=<ID=chr19_KI270865v1_alt,length=52969>
+##contig=<ID=chr19_GL383573v1_alt,length=385657>
+##contig=<ID=chr19_GL383575v2_alt,length=170222>
+##contig=<ID=chr19_GL383576v1_alt,length=188024>
+##contig=<ID=chr19_GL383574v1_alt,length=155864>
+##contig=<ID=chr19_KI270866v1_alt,length=43156>
+##contig=<ID=chr19_KI270867v1_alt,length=233762>
+##contig=<ID=chr19_GL949746v1_alt,length=987716>
+##contig=<ID=chr20_GL383577v2_alt,length=128386>
+##contig=<ID=chr20_KI270869v1_alt,length=118774>
+##contig=<ID=chr20_KI270871v1_alt,length=58661>
+##contig=<ID=chr20_KI270870v1_alt,length=183433>
+##contig=<ID=chr21_GL383578v2_alt,length=63917>
+##contig=<ID=chr21_KI270874v1_alt,length=166743>
+##contig=<ID=chr21_KI270873v1_alt,length=143900>
+##contig=<ID=chr21_GL383579v2_alt,length=201197>
+##contig=<ID=chr21_GL383580v2_alt,length=74653>
+##contig=<ID=chr21_GL383581v2_alt,length=116689>
+##contig=<ID=chr21_KI270872v1_alt,length=82692>
+##contig=<ID=chr22_KI270875v1_alt,length=259914>
+##contig=<ID=chr22_KI270878v1_alt,length=186262>
+##contig=<ID=chr22_KI270879v1_alt,length=304135>
+##contig=<ID=chr22_KI270876v1_alt,length=263666>
+##contig=<ID=chr22_KI270877v1_alt,length=101331>
+##contig=<ID=chr22_GL383583v2_alt,length=96924>
+##contig=<ID=chr22_GL383582v2_alt,length=162811>
+##contig=<ID=chrX_KI270880v1_alt,length=284869>
+##contig=<ID=chrX_KI270881v1_alt,length=144206>
+##contig=<ID=chr19_KI270882v1_alt,length=248807>
+##contig=<ID=chr19_KI270883v1_alt,length=170399>
+##contig=<ID=chr19_KI270884v1_alt,length=157053>
+##contig=<ID=chr19_KI270885v1_alt,length=171027>
+##contig=<ID=chr19_KI270886v1_alt,length=204239>
+##contig=<ID=chr19_KI270887v1_alt,length=209512>
+##contig=<ID=chr19_KI270888v1_alt,length=155532>
+##contig=<ID=chr19_KI270889v1_alt,length=170698>
+##contig=<ID=chr19_KI270890v1_alt,length=184499>
+##contig=<ID=chr19_KI270891v1_alt,length=170680>
+##contig=<ID=chr1_KI270892v1_alt,length=162212>
+##contig=<ID=chr2_KI270894v1_alt,length=214158>
+##contig=<ID=chr2_KI270893v1_alt,length=161218>
+##contig=<ID=chr3_KI270895v1_alt,length=162896>
+##contig=<ID=chr4_KI270896v1_alt,length=378547>
+##contig=<ID=chr5_KI270897v1_alt,length=1144418>
+##contig=<ID=chr5_KI270898v1_alt,length=130957>
+##contig=<ID=chr6_GL000251v2_alt,length=4795265>
+##contig=<ID=chr7_KI270899v1_alt,length=190869>
+##contig=<ID=chr8_KI270901v1_alt,length=136959>
+##contig=<ID=chr8_KI270900v1_alt,length=318687>
+##contig=<ID=chr11_KI270902v1_alt,length=106711>
+##contig=<ID=chr11_KI270903v1_alt,length=214625>
+##contig=<ID=chr12_KI270904v1_alt,length=572349>
+##contig=<ID=chr15_KI270906v1_alt,length=196384>
+##contig=<ID=chr15_KI270905v1_alt,length=5161414>
+##contig=<ID=chr17_KI270907v1_alt,length=137721>
+##contig=<ID=chr17_KI270910v1_alt,length=157099>
+##contig=<ID=chr17_KI270909v1_alt,length=325800>
+##contig=<ID=chr17_JH159148v1_alt,length=88070>
+##contig=<ID=chr17_KI270908v1_alt,length=1423190>
+##contig=<ID=chr18_KI270912v1_alt,length=174061>
+##contig=<ID=chr18_KI270911v1_alt,length=157710>
+##contig=<ID=chr19_GL949747v2_alt,length=729520>
+##contig=<ID=chr22_KB663609v1_alt,length=74013>
+##contig=<ID=chrX_KI270913v1_alt,length=274009>
+##contig=<ID=chr19_KI270914v1_alt,length=205194>
+##contig=<ID=chr19_KI270915v1_alt,length=170665>
+##contig=<ID=chr19_KI270916v1_alt,length=184516>
+##contig=<ID=chr19_KI270917v1_alt,length=190932>
+##contig=<ID=chr19_KI270918v1_alt,length=123111>
+##contig=<ID=chr19_KI270919v1_alt,length=170701>
+##contig=<ID=chr19_KI270920v1_alt,length=198005>
+##contig=<ID=chr19_KI270921v1_alt,length=282224>
+##contig=<ID=chr19_KI270922v1_alt,length=187935>
+##contig=<ID=chr19_KI270923v1_alt,length=189352>
+##contig=<ID=chr3_KI270924v1_alt,length=166540>
+##contig=<ID=chr4_KI270925v1_alt,length=555799>
+##contig=<ID=chr6_GL000252v2_alt,length=4604811>
+##contig=<ID=chr8_KI270926v1_alt,length=229282>
+##contig=<ID=chr11_KI270927v1_alt,length=218612>
+##contig=<ID=chr19_GL949748v2_alt,length=1064304>
+##contig=<ID=chr22_KI270928v1_alt,length=176103>
+##contig=<ID=chr19_KI270929v1_alt,length=186203>
+##contig=<ID=chr19_KI270930v1_alt,length=200773>
+##contig=<ID=chr19_KI270931v1_alt,length=170148>
+##contig=<ID=chr19_KI270932v1_alt,length=215732>
+##contig=<ID=chr19_KI270933v1_alt,length=170537>
+##contig=<ID=chr19_GL000209v2_alt,length=177381>
+##contig=<ID=chr3_KI270934v1_alt,length=163458>
+##contig=<ID=chr6_GL000253v2_alt,length=4677643>
+##contig=<ID=chr19_GL949749v2_alt,length=1091841>
+##contig=<ID=chr3_KI270935v1_alt,length=197351>
+##contig=<ID=chr6_GL000254v2_alt,length=4827813>
+##contig=<ID=chr19_GL949750v2_alt,length=1066390>
+##contig=<ID=chr3_KI270936v1_alt,length=164170>
+##contig=<ID=chr6_GL000255v2_alt,length=4606388>
+##contig=<ID=chr19_GL949751v2_alt,length=1002683>
+##contig=<ID=chr3_KI270937v1_alt,length=165607>
+##contig=<ID=chr6_GL000256v2_alt,length=4929269>
+##contig=<ID=chr19_GL949752v1_alt,length=987100>
+##contig=<ID=chr6_KI270758v1_alt,length=76752>
+##contig=<ID=chr19_GL949753v2_alt,length=796479>
+##contig=<ID=chr19_KI270938v1_alt,length=1066800>
+##contig=<ID=chrM,length=16569>
+##contig=<ID=chrUn_KI270302v1,length=2274>
+##contig=<ID=chrUn_KI270304v1,length=2165>
+##contig=<ID=chrUn_KI270303v1,length=1942>
+##contig=<ID=chrUn_KI270305v1,length=1472>
+##contig=<ID=chrUn_KI270322v1,length=21476>
+##contig=<ID=chrUn_KI270320v1,length=4416>
+##contig=<ID=chrUn_KI270310v1,length=1201>
+##contig=<ID=chrUn_KI270316v1,length=1444>
+##contig=<ID=chrUn_KI270315v1,length=2276>
+##contig=<ID=chrUn_KI270312v1,length=998>
+##contig=<ID=chrUn_KI270311v1,length=12399>
+##contig=<ID=chrUn_KI270317v1,length=37690>
+##contig=<ID=chrUn_KI270412v1,length=1179>
+##contig=<ID=chrUn_KI270411v1,length=2646>
+##contig=<ID=chrUn_KI270414v1,length=2489>
+##contig=<ID=chrUn_KI270419v1,length=1029>
+##contig=<ID=chrUn_KI270418v1,length=2145>
+##contig=<ID=chrUn_KI270420v1,length=2321>
+##contig=<ID=chrUn_KI270424v1,length=2140>
+##contig=<ID=chrUn_KI270417v1,length=2043>
+##contig=<ID=chrUn_KI270422v1,length=1445>
+##contig=<ID=chrUn_KI270423v1,length=981>
+##contig=<ID=chrUn_KI270425v1,length=1884>
+##contig=<ID=chrUn_KI270429v1,length=1361>
+##contig=<ID=chrUn_KI270442v1,length=392061>
+##contig=<ID=chrUn_KI270466v1,length=1233>
+##contig=<ID=chrUn_KI270465v1,length=1774>
+##contig=<ID=chrUn_KI270467v1,length=3920>
+##contig=<ID=chrUn_KI270435v1,length=92983>
+##contig=<ID=chrUn_KI270438v1,length=112505>
+##contig=<ID=chrUn_KI270468v1,length=4055>
+##contig=<ID=chrUn_KI270510v1,length=2415>
+##contig=<ID=chrUn_KI270509v1,length=2318>
+##contig=<ID=chrUn_KI270518v1,length=2186>
+##contig=<ID=chrUn_KI270508v1,length=1951>
+##contig=<ID=chrUn_KI270516v1,length=1300>
+##contig=<ID=chrUn_KI270512v1,length=22689>
+##contig=<ID=chrUn_KI270519v1,length=138126>
+##contig=<ID=chrUn_KI270522v1,length=5674>
+##contig=<ID=chrUn_KI270511v1,length=8127>
+##contig=<ID=chrUn_KI270515v1,length=6361>
+##contig=<ID=chrUn_KI270507v1,length=5353>
+##contig=<ID=chrUn_KI270517v1,length=3253>
+##contig=<ID=chrUn_KI270529v1,length=1899>
+##contig=<ID=chrUn_KI270528v1,length=2983>
+##contig=<ID=chrUn_KI270530v1,length=2168>
+##contig=<ID=chrUn_KI270539v1,length=993>
+##contig=<ID=chrUn_KI270538v1,length=91309>
+##contig=<ID=chrUn_KI270544v1,length=1202>
+##contig=<ID=chrUn_KI270548v1,length=1599>
+##contig=<ID=chrUn_KI270583v1,length=1400>
+##contig=<ID=chrUn_KI270587v1,length=2969>
+##contig=<ID=chrUn_KI270580v1,length=1553>
+##contig=<ID=chrUn_KI270581v1,length=7046>
+##contig=<ID=chrUn_KI270579v1,length=31033>
+##contig=<ID=chrUn_KI270589v1,length=44474>
+##contig=<ID=chrUn_KI270590v1,length=4685>
+##contig=<ID=chrUn_KI270584v1,length=4513>
+##contig=<ID=chrUn_KI270582v1,length=6504>
+##contig=<ID=chrUn_KI270588v1,length=6158>
+##contig=<ID=chrUn_KI270593v1,length=3041>
+##contig=<ID=chrUn_KI270591v1,length=5796>
+##contig=<ID=chrUn_KI270330v1,length=1652>
+##contig=<ID=chrUn_KI270329v1,length=1040>
+##contig=<ID=chrUn_KI270334v1,length=1368>
+##contig=<ID=chrUn_KI270333v1,length=2699>
+##contig=<ID=chrUn_KI270335v1,length=1048>
+##contig=<ID=chrUn_KI270338v1,length=1428>
+##contig=<ID=chrUn_KI270340v1,length=1428>
+##contig=<ID=chrUn_KI270336v1,length=1026>
+##contig=<ID=chrUn_KI270337v1,length=1121>
+##contig=<ID=chrUn_KI270363v1,length=1803>
+##contig=<ID=chrUn_KI270364v1,length=2855>
+##contig=<ID=chrUn_KI270362v1,length=3530>
+##contig=<ID=chrUn_KI270366v1,length=8320>
+##contig=<ID=chrUn_KI270378v1,length=1048>
+##contig=<ID=chrUn_KI270379v1,length=1045>
+##contig=<ID=chrUn_KI270389v1,length=1298>
+##contig=<ID=chrUn_KI270390v1,length=2387>
+##contig=<ID=chrUn_KI270387v1,length=1537>
+##contig=<ID=chrUn_KI270395v1,length=1143>
+##contig=<ID=chrUn_KI270396v1,length=1880>
+##contig=<ID=chrUn_KI270388v1,length=1216>
+##contig=<ID=chrUn_KI270394v1,length=970>
+##contig=<ID=chrUn_KI270386v1,length=1788>
+##contig=<ID=chrUn_KI270391v1,length=1484>
+##contig=<ID=chrUn_KI270383v1,length=1750>
+##contig=<ID=chrUn_KI270393v1,length=1308>
+##contig=<ID=chrUn_KI270384v1,length=1658>
+##contig=<ID=chrUn_KI270392v1,length=971>
+##contig=<ID=chrUn_KI270381v1,length=1930>
+##contig=<ID=chrUn_KI270385v1,length=990>
+##contig=<ID=chrUn_KI270382v1,length=4215>
+##contig=<ID=chrUn_KI270376v1,length=1136>
+##contig=<ID=chrUn_KI270374v1,length=2656>
+##contig=<ID=chrUn_KI270372v1,length=1650>
+##contig=<ID=chrUn_KI270373v1,length=1451>
+##contig=<ID=chrUn_KI270375v1,length=2378>
+##contig=<ID=chrUn_KI270371v1,length=2805>
+##contig=<ID=chrUn_KI270448v1,length=7992>
+##contig=<ID=chrUn_KI270521v1,length=7642>
+##contig=<ID=chrUn_GL000195v1,length=182896>
+##contig=<ID=chrUn_GL000219v1,length=179198>
+##contig=<ID=chrUn_GL000220v1,length=161802>
+##contig=<ID=chrUn_GL000224v1,length=179693>
+##contig=<ID=chrUn_KI270741v1,length=157432>
+##contig=<ID=chrUn_GL000226v1,length=15008>
+##contig=<ID=chrUn_GL000213v1,length=164239>
+##contig=<ID=chrUn_KI270743v1,length=210658>
+##contig=<ID=chrUn_KI270744v1,length=168472>
+##contig=<ID=chrUn_KI270745v1,length=41891>
+##contig=<ID=chrUn_KI270746v1,length=66486>
+##contig=<ID=chrUn_KI270747v1,length=198735>
+##contig=<ID=chrUn_KI270748v1,length=93321>
+##contig=<ID=chrUn_KI270749v1,length=158759>
+##contig=<ID=chrUn_KI270750v1,length=148850>
+##contig=<ID=chrUn_KI270751v1,length=150742>
+##contig=<ID=chrUn_KI270752v1,length=27745>
+##contig=<ID=chrUn_KI270753v1,length=62944>
+##contig=<ID=chrUn_KI270754v1,length=40191>
+##contig=<ID=chrUn_KI270755v1,length=36723>
+##contig=<ID=chrUn_KI270756v1,length=79590>
+##contig=<ID=chrUn_KI270757v1,length=71251>
+##contig=<ID=chrUn_GL000214v1,length=137718>
+##contig=<ID=chrUn_KI270742v1,length=186739>
+##contig=<ID=chrUn_GL000216v2,length=176608>
+##contig=<ID=chrUn_GL000218v1,length=161147>
+##contig=<ID=chrX,length=156040895>
+##contig=<ID=chrY,length=57227415>
+##contig=<ID=chrY_KI270740v1_random,length=37240>
+##phasing=none
+##commandline= "freebayes  --region  chrY_KI270740v1_random:0..37240  --bam  b_0.bam  --fasta-reference  /panfs/roc/rissdb/galaxy/genomes/hg38/seq/hg38.fa  --vcf  ./vcf_output/part_chrY_KI270740v1_random:0..37240.vcf "
+##INFO=<ID=NS,Number=1,Type=Integer,Description= "Number  of  samples  with  data ">
+##INFO=<ID=DP,Number=1,Type=Integer,Description= "Total  read  depth  at  the  locus ">
+##INFO=<ID=DPB,Number=1,Type=Float,Description= "Total  read  depth  per  bp  at  the  locus;  bases  in  reads  overlapping  /  bases  in  haplotype ">
+##INFO=<ID=AC,Number=A,Type=Integer,Description= "Total  number  of  alternate  alleles  in  called  genotypes ">
+##INFO=<ID=AN,Number=1,Type=Integer,Description= "Total  number  of  alleles  in  called  genotypes ">
+##INFO=<ID=AF,Number=A,Type=Float,Description= "Estimated  allele  frequency  in  the  range  (0,1] ">
+##INFO=<ID=RO,Number=1,Type=Integer,Description= "Count  of  full  observations  of  the  reference  haplotype. ">
+##INFO=<ID=AO,Number=A,Type=Integer,Description= "Count  of  full  observations  of  this  alternate  haplotype. ">
+##INFO=<ID=PRO,Number=1,Type=Float,Description= "Reference  allele  observation  count,  with  partial  observations  recorded  fractionally ">
+##INFO=<ID=PAO,Number=A,Type=Float,Description= "Alternate  allele  observations,  with  partial  observations  recorded  fractionally ">
+##INFO=<ID=QR,Number=1,Type=Integer,Description= "Reference  allele  quality  sum  in  phred ">
+##INFO=<ID=QA,Number=A,Type=Integer,Description= "Alternate  allele  quality  sum  in  phred ">
+##INFO=<ID=PQR,Number=1,Type=Float,Description= "Reference  allele  quality  sum  in  phred  for  partial  observations ">
+##INFO=<ID=PQA,Number=A,Type=Float,Description= "Alternate  allele  quality  sum  in  phred  for  partial  observations ">
+##INFO=<ID=SRF,Number=1,Type=Integer,Description= "Number  of  reference  observations  on  the  forward  strand ">
+##INFO=<ID=SRR,Number=1,Type=Integer,Description= "Number  of  reference  observations  on  the  reverse  strand ">
+##INFO=<ID=SAF,Number=A,Type=Integer,Description= "Number  of  alternate  observations  on  the  forward  strand ">
+##INFO=<ID=SAR,Number=A,Type=Integer,Description= "Number  of  alternate  observations  on  the  reverse  strand ">
+##INFO=<ID=SRP,Number=1,Type=Float,Description= "Strand  balance  probability  for  the  reference  allele:  Phred-scaled  upper-bounds  estimate  of  the  probability  of  observing  the  deviation  between  SRF  and  SRR  given  E(SRF/SRR)  ~  0.5,  derived  using  Hoeffding's  inequality ">
+##INFO=<ID=SAP,Number=A,Type=Float,Description= "Strand  balance  probability  for  the  alternate  allele:  Phred-scaled  upper-bounds  estimate  of  the  probability  of  observing  the  deviation  between  SAF  and  SAR  given  E(SAF/SAR)  ~  0.5,  derived  using  Hoeffding's  inequality ">
+##INFO=<ID=AB,Number=A,Type=Float,Description= "Allele  balance  at  heterozygous  sites:  a  number  between  0  and  1  representing  the  ratio  of  reads  showing  the  reference  allele  to  all  reads,  considering  only  reads  from  individuals  called  as  heterozygous ">
+##INFO=<ID=ABP,Number=A,Type=Float,Description= "Allele  balance  probability  at  heterozygous  sites:  Phred-scaled  upper-bounds  estimate  of  the  probability  of  observing  the  deviation  between  ABR  and  ABA  given  E(ABR/ABA)  ~  0.5,  derived  using  Hoeffding's  inequality ">
+##INFO=<ID=RUN,Number=A,Type=Integer,Description= "Run  length:  the  number  of  consecutive  repeats  of  the  alternate  allele  in  the  reference  genome ">
+##INFO=<ID=RPP,Number=A,Type=Float,Description= "Read  Placement  Probability:  Phred-scaled  upper-bounds  estimate  of  the  probability  of  observing  the  deviation  between  RPL  and  RPR  given  E(RPL/RPR)  ~  0.5,  derived  using  Hoeffding's  inequality ">
+##INFO=<ID=RPPR,Number=1,Type=Float,Description= "Read  Placement  Probability  for  reference  observations:  Phred-scaled  upper-bounds  estimate  of  the  probability  of  observing  the  deviation  between  RPL  and  RPR  given  E(RPL/RPR)  ~  0.5,  derived  using  Hoeffding's  inequality ">
+##INFO=<ID=RPL,Number=A,Type=Float,Description= "Reads  Placed  Left:  number  of  reads  supporting  the  alternate  balanced  to  the  left  (5')  of  the  alternate  allele ">
+##INFO=<ID=RPR,Number=A,Type=Float,Description= "Reads  Placed  Right:  number  of  reads  supporting  the  alternate  balanced  to  the  right  (3')  of  the  alternate  allele ">
+##INFO=<ID=EPP,Number=A,Type=Float,Description= "End  Placement  Probability:  Phred-scaled  upper-bounds  estimate  of  the  probability  of  observing  the  deviation  between  EL  and  ER  given  E(EL/ER)  ~  0.5,  derived  using  Hoeffding's  inequality ">
+##INFO=<ID=EPPR,Number=1,Type=Float,Description= "End  Placement  Probability  for  reference  observations:  Phred-scaled  upper-bounds  estimate  of  the  probability  of  observing  the  deviation  between  EL  and  ER  given  E(EL/ER)  ~  0.5,  derived  using  Hoeffding's  inequality ">
+##INFO=<ID=DPRA,Number=A,Type=Float,Description= "Alternate  allele  depth  ratio.    Ratio  between  depth  in  samples  with  each  called  alternate  allele  and  those  without. ">
+##INFO=<ID=ODDS,Number=1,Type=Float,Description= "The  log  odds  ratio  of  the  best  genotype  combination  to  the  second-best. ">
+##INFO=<ID=GTI,Number=1,Type=Integer,Description= "Number  of  genotyping  iterations  required  to  reach  convergence  or  bailout. ">
+##INFO=<ID=TYPE,Number=A,Type=String,Description= "The  type  of  allele,  either  snp,  mnp,  ins,  del,  or  complex. ">
+##INFO=<ID=CIGAR,Number=A,Type=String,Description= "The  extended  CIGAR  representation  of  each  alternate  allele,  with  the  exception  that  '='  is  replaced  by  'M'  to  ease  VCF  parsing.    Note  that  INDEL  alleles  do  not  have  the  first  matched  base  (which  is  provided  by  default,  per  the  spec)  referred  to  by  the  CIGAR. ">
+##INFO=<ID=NUMALT,Number=1,Type=Integer,Description= "Number  of  unique  non-reference  alleles  in  called  genotypes  at  this  position. ">
+##INFO=<ID=MEANALT,Number=A,Type=Float,Description= "Mean  number  of  unique  non-reference  allele  observations  per  sample  with  the  corresponding  alternate  alleles. ">
+##INFO=<ID=LEN,Number=A,Type=Integer,Description= "allele  length ">
+##INFO=<ID=MQM,Number=A,Type=Float,Description= "Mean  mapping  quality  of  observed  alternate  alleles ">
+##INFO=<ID=MQMR,Number=1,Type=Float,Description= "Mean  mapping  quality  of  observed  reference  alleles ">
+##INFO=<ID=PAIRED,Number=A,Type=Float,Description= "Proportion  of  observed  alternate  alleles  which  are  supported  by  properly  paired  read  fragments ">
+##INFO=<ID=PAIREDR,Number=1,Type=Float,Description= "Proportion  of  observed  reference  alleles  which  are  supported  by  properly  paired  read  fragments ">
+##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description= "Minimum  depth  in  gVCF  output  block. ">
+##INFO=<ID=END,Number=1,Type=Integer,Description= "Last  position  (inclusive)  in  gVCF  output  record. ">
+##FORMAT=<ID=GT,Number=1,Type=String,Description= "Genotype ">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description= "Genotype  Quality,  the  Phred-scaled  marginal  (or  unconditional)  probability  of  the  called  genotype ">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description= "Genotype  Likelihood,  log10-scaled  likelihoods  of  the  data  given  the  called  genotype  for  each  possible  genotype  generated  from  the  reference  and  alternate  alleles  given  the  sample  ploidy ">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description= "Read  Depth ">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description= "Number  of  observation  for  each  allele ">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description= "Reference  allele  observation  count ">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description= "Sum  of  quality  of  the  reference  observations ">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description= "Alternate  allele  observation  count ">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description= "Sum  of  quality  of  the  alternate  observations ">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description= "Minimum  depth  in  gVCF  output  block. ">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	unknown
+chr19	18856059	.	C	T	10269.5	.	AB=0.248844;ABP=1306.46;AC=1;AF=0.5;AN=2;AO=592;CIGAR=1X;DP=2379;DPB=2379;DPRA=0;EPP=30.139;EPPR=172.262;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=59.9339;NS=1;NUMALT=1;ODDS=2364.65;PAIRED=0.991554;PAIREDR=0.983754;PAO=0;PQA=0;PQR=0;PRO=0;QA=21546;QR=64865;RO=1785;RPL=120;RPP=457.494;RPPR=1043.89;RPR=472;RUN=1;SAF=303;SAP=3.72923;SAR=289;SRF=873;SRP=4.86061;SRR=912;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:2379:1785,592:1785:64865:592:21546:-1222.54,0,-5112.92