Truncating BAM Files
Hello,
I am trying to create a smaller BAM file from the original BAM file. The smaller BAM file should have info on only about 10 loci.
Can I not just append the mpileup() output of the region of interest to the header (samtools view -H <bam>)?
Any pointers on how I can accomplish this would be appreciated!
Thanks
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samtools view with option '-L your.bed' http://www.htslib.org/doc/samtools.html
Sorry, but I don't have a .bed file. Just a BAM.
I executed the following but I get no output.
That's not a bed file.
echo -e "Chr1\t3631\t5899" > test.bedwould make a valid BED file.