How to get the normal coverage of the reference allele in all.somatic.indels.vcf file?
jane.me...@gmail.com
I am using Strelka 1.0.14 on WGS data for a few days.
Strelka ran without problem on my samples.
To further filtered my list of variants, I need information about the coverage of reference and "variant" alleles in both normal and tumor samples.
As I read in this discussion list, the number of reads supporting the "indel"(=variant) allele is given by the TIR column (its first field preferentially).
My problem is to find the number of reads supporting the reference allele.
Maybe I missed something, but I tried DP, TAR, DP-TOR, TAR+TOR,... without success....
In some cases, DP seem ok. In other cases, TAR+TOR look ok.
This information is crucial for my analysis and I am stuck here with this detail...
Could you please tell how to compute precisely the number of reads supporting the reference allele?
Thank you in advance,
Jane
Saunders, Chris
The closest number to what you’re looking for is “TAR”. Strictly this is reads strongly support the reference allele or an alternate overlapping indel. So TIR/(TIR+TAR) will give you approximately “fraction of reads supporting the variant allele among all reads strongly supporting one local haplotype”. TAR might not “look” like the right value in some contexts compared to the way reads appear in IGV because of local repeat structures – many reads provide very similar support to two or more alleles even though they’re mapped/appear in IGV in such a way so as to apparently support the reference.
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