GatherSampleEvidence
Runs raw evidence collection on each sample with the following SV callers: Manta, Wham, Scramble, and/or MELT. For guidance on pre-filtering prior to GatherSampleEvidence, refer to the Sample Exclusion section.
The following diagram illustrates the downstream workflows of the GatherSampleEvidence workflow
in the recommended invocation order. You may refer to
this diagram
for the overall recommended invocation order.
Inputs
bam_or_cram_file
A BAM or CRAM file aligned to hg38. Index file (.bai) must be provided if using BAM.
sample_id
Refer to the sample ID requirements for specifications of allowable sample IDs. IDs that do not meet these requirements may cause errors.
preprocessed_intervals
Picard interval list.
sd_locs_vcf
(sd: site depth)
A VCF file containing allele counts at common SNP loci of the genome, which is used for calculating BAF.
For human genome, you may use dbSNP
that contains a complete list of common and clinical human single nucleotide variations,
microsatellites, and small-scale insertions and deletions.
You may find a link to the file in
this reference.
Outputs
- Binned read counts file
- Split reads (SR) file
- Discordant read pairs (PE) file
manta_vcf
A VCF file containing variants called by Manta.
melt_vcf
A VCF file containing variants called by MELT.
scramble_vcf
A VCF file containing variants called by Scramble.
wham_vcf
A VCF file containing variants called by Wham.