samtools/bcftools: How to inspect SNPs not made it into vcf file

[muenalan]

Hi,

Is there any parameter to "log" the snp-calling for individual SNP's which did not make it into the .vcf ? Or any other way to look how are the parameters for that SNP, if called ?

Info: We generate our vcf's like this:

samtools mpileup -ugf 'human_build37_ucsc.fa' 'test.bam' | bcftools view -bvcg - > 'test.bam.bcf'
bcftools view 'test.bam.bcf' > 'test.bam.bcf.vcf'


Thx,
muenalan

[AWeller]

I'm not sure if I understand your question correctly.

In general, omitting the "-v" in bcftools will show you all positions, not just the variants.

A convenient way to manually inspect a single position that didn't get called is the "samtools mpileup -r" option, where eg "samtools mpileup -r CHROMOSOMEII:10-10 ..." will show you only this one location.

If you are talking about doing this in bulk for the whole genome, a possibility is to do a second pileup of all positions and then find the differences via "diff" or a custom script.

Hope to help,

best
Andreas

[muenalan]

[solved]

Yes,

Exactly the information I was looking for.

Thx,
M!