Question: Samtools Mpileup Defined Regions
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Vova Naumov • 210 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?
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modified 4.9 years ago
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swbarnes2 ♦ 3.9k
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4.9 years ago by
Vova Naumov • 210
Please take a closer look at mpileup in samtools. The documentation clearly states how to call variants and use a bed file.
Thank's a lot but an example would be very helpful