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JaneliaSciComp / msg

Multiplexed Shotgun Genotyping
http://genomics.princeton.edu/AndolfattoLab/MSG.html
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msg.pl - updating genomes step - samtools view command references missing var #21

Closed gregpinero closed 12 years ago

gregpinero commented 12 years ago

It appears that when this line is called: &system_call("samtools", "view", "-bt", "$genomes{$sp}.msg.fai", "-o $out.bam", "$out.filtered.sam") ;

That %genomes has not been defined yet. This creates a command where the fai file doesn't exist.

The bam file is still created so I'm not sure what adverse effect this is having but it's worth investigating.

Maybe it is a typo and was intended to say genomes_fa?

We should probably always use strict mode in Perl to avoid issues like this.

gregpinero commented 12 years ago

It looks like that missing file is the ref list:

-t FILE This file is TAB-delimited. Each line must contain the reference name and the length of the reference, one line for each distinct reference; additional fields are ignored. This file also defines the order of the reference sequences in sorting. If you run ‘samtools faidx ’, the resultant index file .fai can be used as this file.

from http://samtools.sourceforge.net/samtools.shtml