[HTSlib] cannot find htscmd

Question

[anon]

Hi All,

this may be a stupid question, but after installing and compiling the htslib, I can't find the htscmd in the directory, it seems like just htsfile, tabix etc. are installed. I would like to use it for shuffle the reads in my bam file. What am I doing wrong?

Thanks!

Answer 1

[Devon Ryan]

htscmd was moved to bcftools in July 2013. Having said that, you might just mention what you're trying to do, since the actual functionality that you're after may be elsewhere still.

[anon]

I just followed the GATK instructions here: http://gatkforums.broadinstitute.org/discussion/2908/howto-revert-a-bam-file-to-fastq-format , and didn't check any related information (neither even the comments...). Many thanks!

[Devon Ryan]

Ah, that functionality is in samtools then (the functions are otherwise named the same).