Split a sam file by chromosome
1
0
Entering edit mode
10 days ago
ICfc97 • 0

Hi! I'm trying to use PRISM program to detect CNVs and the input files have to be .SAM files for each chromosome, I have the .BAM file of each sample but I don't know it it is convenient to convert it to .SAM and the n split it or the contrary.

for file in *_chr.bam; do
filename=echo $file | cut -d “.” -f 1; for chrom in seq 1 22 X Y; do samtools view -bh$file chr${chrom} >${filename}_${chrom}.bam; done; done CNVs NGS PRISM • 113 views ADD COMMENT 1 Entering edit mode If you want SAM files the use: samtools view -h$file chr${chrom} >${filename}_\${chrom}.sam;
0
Entering edit mode
10 days ago
GenoMax 102k

While some commands have changed over years this should still be useful: How Can I Split Bam Into Chromosome (In A Loop) Using Samtools?

Sounds like you know what you want and how to get there.