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Danny Antaki edited this page Nov 17, 2017 · 25 revisions
  1. BAM
  2. SV Files
  3. SNV VCF
  4. PED
sv2 -i in.bam -b sv.bed -p fam.ped -snv in.vcf

BAM

-i, -bam    ...    BAM file(s)

BAM/CRAM files must contain supplementary alignment tags (SA) that flag chimeric reads (split-reads). Without SA tags, SV2 will not genotype variants well.

SV2 requires indexed BAMs/CRAMs with the index file in the same directory as the BAM/CRAM file.

SV2 expects a sample name (@RG SM:<sample_name>) in the header. Sample names must be match ids in PED and SNV VCF files.

SV2 supports BAM/CRAM files that were aligned using the bwa mem -M option. Pass the -M flag to the SV2 command to genotype samples that used the legacy -M option. Details here

SV Input

-b, -bed    ...    BED file(s)

-v, -vcf    ...    VCF file(s)

SV2 requires either BED or VCF files of deletions and duplications.

Users can submit multiple BED or VCF files, separating each file with a space

-b del.bed dup.bed -v del.vcf

BED Input

BED files must be either space or tab delimited with at least four columns, extra columns are ignored. SV type must be contain either DEL or DUP.

Required format for BED files

CHROM START END SV TYPE
chr1 100 200 DEL_ALU
chr1 500 1000 DUP

Failure to format this file correctly will result in a warning or Segmentation Fault. See Troubleshooting

VCF Input

VCF files can be either compressed (.gz) or uncompressed. VCF files must contain both END= and SVTYPE= in the INFO column. SVTYPE= must contain either DEL or DUP.

SNV VCF

-snv    ...    SNV VCF(s)

SNV VCF files must contain allele depth encoded as either AD or DPR in the format column. Additionally, VCF files must be compressed with bgzip and indexed with tabix.

VCFs from FreeBayes and GATK are compatible with SV2

SNV information is leverage for genotyping duplications that are between repetitive sequence; typically such SVs lack split-reads or discordant paired-ends.

PED

-p, -ped    ...    PED file(s)

PED format defined by plink

SV2 processes the individual ID and gender columns, extra columns are ignored

Gender is 1 male and 2 for female

Family ID Individual ID Paternal ID Maternal ID Gender
0 HG00096 0 0 1
0 NA12878 0 0 2
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