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svtyper (version 0.1.1)

vcf file:

VCF input (default: stdin)

bam/cram file:

BAM or CRAM file(s), comma-separated if genotyping multiple samples

Reference:

Indexed reference FASTA file (recommended for reading CRAM files)

Library json file:

read JSON file of library information

Min aligned bases:

minimum number of aligned bases to consider read as evidence [20]

Sampling size for insert size determination:

number of reads to sample from BAM file for building insert size distribution [1000000]

Add genotyping quality:

add genotyping quality to existing QUAL (default: overwrite QUAL field)

Max reads to consider per variant:

maximum number of reads to assess at any variant (reduces processing time in high-depth regions, default: 0 = unlimited)

Split read weight:

weight for split reads [1]

Discordant read weight:

weight for discordant paired-end reads [1]

Create an output library json file:

if an input library json file (--lib_info) is not provided, create an output library json file

Create an output bam file:

generate an output bam file containing the reads supporting the structural variants

usage: svtyper [-h] [-i FILE] [-o FILE] -B FILE [-T FILE] [-l FILE] [-m INT]

[-n INT] [-q] [--max_reads INT] [--split_weight FLOAT] [--disc_weight FLOAT] [-w FILE] [--verbose]

svtyper author: Colby Chiang (colbychiang@wustl.edu) version: v0.6.0 description: Compute genotype of structural variants based on breakpoint depth

optional arguments:

-h, --help show this help message and exit

-i FILE, --input_vcf FILE

VCF input (default: stdin)

-o FILE, --output_vcf FILE

output VCF to write (default: stdout)

-B FILE, --bam FILE

BAM or CRAM file(s), comma-separated if genotyping multiple samples

-T FILE, --ref_fasta FILE

Indexed reference FASTA file (recommended for reading CRAM files)

-l FILE, --lib_info FILE

create/read JSON file of library information

-m INT, --min_aligned INT

minimum number of aligned bases to consider read as evidence [20]

-n INT number of reads to sample from BAM file for building insert size distribution [1000000]

-q, --sum_quals

add genotyping quality to existing QUAL (default: overwrite QUAL field)

--max_reads INT

maximum number of reads to assess at any variant (reduces processing time in high-depth regions, default: unlimited)

--split_weight FLOAT

weight for split reads [1]

--disc_weight FLOAT

weight for discordant paired-end reads [1]

-w FILE, --write_alignment FILE

write relevant reads to BAM file

--verbose Report status updates

`-h, --help`	show this help message and exit
`-i FILE, --input_vcf FILE`
	VCF input (default: stdin)
`-o FILE, --output_vcf FILE`
	output VCF to write (default: stdout)
`-B FILE, --bam FILE`
	BAM or CRAM file(s), comma-separated if genotyping multiple samples
`-T FILE, --ref_fasta FILE`
	Indexed reference FASTA file (recommended for reading CRAM files)
`-l FILE, --lib_info FILE`
	create/read JSON file of library information
`-m INT, --min_aligned INT`
	minimum number of aligned bases to consider read as evidence [20]
`-n INT`	number of reads to sample from BAM file for building insert size distribution [1000000]
`-q, --sum_quals`
	add genotyping quality to existing QUAL (default: overwrite QUAL field)
`--max_reads INT`
	maximum number of reads to assess at any variant (reduces processing time in high-depth regions, default: unlimited)
`--split_weight FLOAT`
	weight for split reads [1]
`--disc_weight FLOAT`
	weight for discordant paired-end reads [1]
`-w FILE, --write_alignment FILE`
	write relevant reads to BAM file
`--verbose`	Report status updates