Allele Frequency reported by Samtools and IGV Do Not Agree

Question

[OmBibo]

Hi all,

I use the mpileup command to create the pileup file with this command :

samtools mpileup -v -u -f file.fasta mybam.bam -l my bed.bed > myvcf.vcf

The problem is that When I visualize a region using IGV, the allele frequency percentage reported by IGV does not agree with that reported by the mpileup command (the QS values) in any given position. Has anyone else faced this problem? Is there a solution?

Thank you,

Answer 1

[shiyang_bio]

It's possibly a result of the filter in samtools. By default samtools discards some reads with low quality while IGV utilized all reads. You may check the parameters for samtools and include all reads.

[OmBibo]

Thanks Shiyang for your reply. For samtools, I used --min-BQ 0 to disable filtering of low-quality bases. But no changes, it shows the same values as outputs. Please if you have any idea about other parameters or filters to consider for samtools? Your help is really appreciated.

[shiyang_bio]

So sorry that I haven't much experience on it. But I think this link may help you Depth Of Coverage Reported By Igv And Samtools Do Not Agree