bcftools 1.4.1 call parameters

Question

[cetin.m]

I first do samtools mpileup:

samtools mpileup -uf /mnt/NAS/share/Ref/human/hs37d5.fa -l 1000G.bed -q 30 -Q 30 in.bam -o out.bcf

Then: I can call snps from the bcf with at least two different commands:

bcftools call -mV indels
bcftools call -c -v

I get two vastly different results with these.

I don't know which one is correct and how I should actually do this.

Any suggestions?

Answer 1

[finswimmer]

Hello cetin.m ,

first of all: Try to update. Current release is v1.9. And there samtools mpileup is deprecated. Use bcftools mpileup instead.

-m and -c activate different algorithm for calling variants. -c is the older one. Unless you have very good reasons you should use -m.

In your first command you skip variant calling for indels, but not in your second. So of course you have than different between your results.

fin swimmer