Number of SNPs and Indels doesn't match with the numbers reported in README files about pipelines

[Rohit-Satyam]

@jessicaway @alimanfoo Can you guys help me with this?

[alimanfoo]

Hi @podpearson, would you be able to help here?

[podpearson]

Dear @Rohit-Satyam

I think you might be seeing different numbers of SNPs/indels from what we report in the README because bcftools might treat spanning deletion alleles (*) as SNPs rather than indels (see samtools/bcftools#736). You could perhaps try first creating a "SNPs only" VCF using the suggestion in the above link (-e'ALT="*" || type!="snp"' ) and then run bcftools stats on this new file to see if numbers of SNPs match what we report in the README.

I don't tend to monitor this github repo closely, so for future queries, it might be better to email [email protected] which I should see straight away.

HTH, Richard

[Rohit-Satyam]

Yes, you are right. I did as you suggested using bcftools stats -e'ALT="*" || type!="snp"' filter.vcf.gz and the number of SNPs now are 945,649