Tools for working with genomic and high throughput sequencing data.
Group: Unique Molecular Identifiers (UMIs)
Extracts data to make reviewing of variant calls from consensus reads easier. Creates a list of variant sites from the input VCF (SNPs only) or IntervalList then extracts all the consensus reads that do not contain a reference allele at the the variant sites, and all raw reads that contributed to those consensus reads. This will include consensus reads that carry the alternate allele, a third allele, a no-call or a spanning deletion at the variant site.
Reads are correlated between consensus and grouped BAMs using a molecule ID stored
in an optional attribute, MI by default. In order to support paired molecule IDs
where two or more molecule IDs are related (e.g. see the Paired assignment strategy
in GroupReadsByUmi) the molecule ID is truncated at the last / if present
(e.g. 1/A => 1 and 2 => 2).
Both input BAMs must be coordinate sorted and indexed.
A pair of output BAMs named <output>.consensus.bam and <output>.grouped.bam are created
with the relevant reads from each input BAM, and a review file <output>.txt is
created. The review file contains details on each variant position along with detailed
information on each consensus read that supports the variant. If the sample-name argument
is supplied and the input is VCF, genotype information for that sample will be retrieved.
If the sample-name isn’t supplied and the VCF contains only a single sample then those
genotypes will be used.
| Name | Flag | Type | Description | Required? | Max # of Values | Default Value(s) |
|---|---|---|---|---|---|---|
| input | i | FilePath | Input VCF or IntervalList of variant locations. | Required | 1 | |
| sample | s | String | Name of the sample being reviewed. | Optional | 1 | |
| consensus-bam | c | PathToBam | BAM file of consensus reads used to call variants. | Required | 1 | |
| grouped-bam | g | PathToBam | BAM file of grouped raw reads used to build consensuses. | Required | 1 | |
| ref | r | PathToFasta | Reference fasta file. | Required | 1 | |
| output | o | PathPrefix | Basename of output files to create. | Required | 1 | |
| ignore-ns-in-consensus-reads | N | Boolean | Ignore N bases in the consensus reads. | Optional | 1 | false |
| maf | m | Double | Only output detailed information for variants at maf and below. | Optional | 1 | 0.05 |