Mercurial > repos > iuc > lofreq_filter

diff test-data/call-out1.vcf @ 3:701d134358ad draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 0cec5f95ad0b141a9cc5be00be6d2574609b661a"
author iuc
date Fri, 29 May 2020 15:22:09 -0400
parents 6f9ffff040ce
children 950d1d49d678
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--- a/test-data/call-out1.vcf	Sat Mar 21 10:51:28 2020 -0400
+++ b/test-data/call-out1.vcf	Fri May 29 15:22:09 2020 -0400
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.0
-##fileDate=20191125
-##source=lofreq call --verbose --ref reference.fa --sig 0.01 --bonf dynamic --no-default-filter -r pBR322:1-2180 -o /tmp/lofreq2_call_parallel3mrmthi_/0.vcf.gz alignments.bam
+##fileDate=20200529
+##source=lofreq call --verbose --ref reference.fa --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --src-qual --ign-vcf ign0.vcf --def-nm-q 40 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic --no-default-filter -r pBR322:1-2180 -o /tmp/lofreq2_call_parallelqgn6kxdr/0.vcf.gz reads.bam 
 ##reference=reference.fa
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">