reference for samtools mpileup after extracting chromosome from alignment

reference for samtools mpileup after extracting chromosome from alignment

0

Good evening,

I have extracted one chromosome from alignment map (.bam), using samtools view:

samtools view -b map.bam chr1 > map_chr1.bam

Now I would like to prepare file for SNP calling using samtools mpileup. Is it correct to use chr1.fasta as reference file (not full genome)? Like this:

 samtools mpileup -f chr1.fasta -o map_chr1_polym.bcf map_chr1.bam

Of course, after indexing chr1.fasta (using samtools faidx) and getting .fai.

Thank you in advance!

Best regards,
Poecile


reference


mpileup


samtools


alignment


SNP

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