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Question: Samtools Mpileup Defined Regions
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gravatar for Vova Naumov
7.3 years ago by
Vova Naumov • 220
Russia, Moscow
Vova Naumov • 220 wrote:

Hi! I need to get genotypes in a list of positions (for example BED file) having BAM file. Trying to use tool samtools mpileup. I know I can do it by creating consensus fastq using

samtools mpileup -uf hg19.fa file.bam | \
bcftools view -cg - | \
perl vcfutils.pl vcf2fq > consensus.fastq

and then getting genotypes from fastq file, but it's ineffective. Do you know how to get differences from reference, genotype calls at interesting positions simultaneously?
samtools • 3.6k views
ADD COMMENT • link •
modified 7.3 years ago by swbarnes2 ♦ 9.4k • written 7.3 years ago by Vova Naumov • 220
2

Please take a closer look at mpileup in samtools. The documentation clearly states how to call variants and use a bed file.

ADD REPLY • link written 7.3 years ago by Zev.Kronenberg ♦ 11k

Thank's a lot but an example would be very helpful

ADD REPLY • link written 7.3 years ago by Vova Naumov • 220
1
gravatar for swbarnes2
7.3 years ago by
swbarnes2 ♦ 9.4k
United States
swbarnes2 ♦ 9.4k wrote:

I'd use BEDTools intersectBed to get the intersection between your all-points vcf and your bed file coordinates. That's way simpler than making a consensus fastq.

ADD COMMENT • link written 7.3 years ago by swbarnes2 ♦ 9.4k
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