List of variants analysed/used in calculation

[Katie]

Hi,

Not sure whether I saw this as a possible output - but I was wondering whether there is information given about the variant sites that VerifyBamID looks at in the BAM/VCF to make its final contamination calculation (FREEMIX/CHIPMIX)?  We would like to further look at these variants in our highly contaminated samples in some downstream analysis and it will come in handy.

Thanks!

K.

[Sarah]

Hi,

I'd like to re-open this question as it wasn't answered and I would also like to know how we can find out which SNPs are "passing the criteria". I've had a look through the output files and all the documentation but I can't find a way to do it. It would really helpful for troubleshooting to see where the passed SNPs are falling within our target regions.

Thanks

Sarah

[Hyun Min Kang]

There is no passing criteria. You just need to use the markers known to be polymorphic in SNP arrays.

There is no particular way to evaluate the contribution of each variant to contamination in the current software. 

Thanks,

Hyun.

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[Sarah]

Thanks Hyun. However, I'm still confused as the documentation describes the "#SNPs" field as the "# of SNPs passing the criteria from the VCF file". I've been providing a VCF file of SNPs with AF > 1% but the "#SNPs" is far fewer than the number I provide so surely the software is selecting which SNPs to include/exclude?

[Hyun Min Kang]

I believe that it is using the SNPs with at least one coverage. 

Hyun.

On Thu, Aug 30, 2018 at 6:35 AM Sarah <srj...@gmail.com> wrote:

Thanks Hyun. However, I'm still confused as the documentation describes the "#SNPs" field as the "# of SNPs passing the criteria from the VCF file". I've been providing a VCF file of SNPs with AF > 1% but the "#SNPs" is far fewer than the number I provide so surely the software is selecting which SNPs to include/exclude?