Question: bcftools 1.4.1 call parameters
gravatar for cetin.m
9 days ago by
cetin.m10 wrote:

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?

snp call bcftools • 70 views
ADD COMMENTlink modified 9 days ago by finswimmer8.8k • written 9 days ago by cetin.m10
gravatar for finswimmer
9 days ago by
finswimmer8.8k wrote:

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

ADD COMMENTlink written 9 days ago by finswimmer8.8k
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