Change the BAM file sort command for Samtools v1.3+

FelixKrueger / SNPsplit

Allele-specific alignment sorting

http://felixkrueger.github.io/SNPsplit/

GNU General Public License v3.0

52 stars 20 forks source link

Change the BAM file sort command for Samtools v1.3+ #2

Closed FelixKrueger closed 8 years ago

FelixKrueger commented 8 years ago

The Samtools sort command seems to have changed from earlier versions and now fails when using Samtools version 1.3+ with the following error message:

File specified as unsorted paired-end BAM file Sorting BAM file 'test.bam' by read IDs ... [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files

This probably just needs specifically specifying the outfile explicitly.

FelixKrueger commented 8 years ago

Changed the sorting command for samtools sort -n to now include a -o outfile. Fixed in 465501cb062aaa14ca900153e597b41a159d88b1.