I want to compute the depth of coverage only for specific intervals in phase 3, 1000 genomes project.I have not worked with 1000 genomes project before, so a bit unfamiliar with it. I do not want to download all of the bam files for the entire genomic region, just those intervals which I am interested in them. I guess I can use this (I found from biostars forum)
samtools -bu view 'http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG01375/alignment/HG01375.mapped.ILLUMINA.bwa.CLM.low_coverage.20120522.bam' "2:1000000-2000000" | (...)
However, I am just a bit confused. First of all, when I try the code above directly from the command line, I get an error message "No such file or directory"! Am I doing something wrong? or should I provide a specific path?
Second, I want to run it for the mapped files for all individuals:
*.bam”. through a loop.
Can anyone help me to solve my problem?