How are the variants called by samtools?

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8.8 years ago

lakhujanivijay 5.9k

Sorry if this question sounds ridiculous but I am very much puzzled as how variants are called by samtools? I mean what is the correct path?

samtools mpileup created the mpileup file or vcf file which have the variants? What does BAQ does; I suppose it is bundled with samtools, is that correct?

Also, what does bcf tools call function does. I am totally confused at this point; please help

samtools BAQ • 2.1k views

ADD COMMENT • link updated 2.3 years ago by Ram 44k • written 8.8 years ago by lakhujanivijay 5.9k

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Did you mean this?

samtools mpileup -d $coverage_max -L $coverage_max -E -uf reference.fasta input.bam -P ILLUMINA -Q 30 | bcftools view -bvgc - > calls.bcf
bcftools view calls.bcf | vcfutils varFilter -d 30 -a 10 -1 0.001 -2 0.001 -3 0 -4 0.0001 - > calls.vcf

ADD REPLY • link updated 2.3 years ago by Ram 44k • written 8.8 years ago by Max Ivon ▴ 140

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Yes, can you explain it a little bit like what parameter and what tool is doing what?

ADD REPLY • link 8.8 years ago by lakhujanivijay 5.9k

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