reference for samtools mpileup after extracting chromosome from alignment
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
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