Entering edit mode
5.1 years ago
L. A. Liggett ▴ 120
I have been using something like
samtools faidx hg19.fa chr1:115227843-115227863 to extract sequence for specified locations. However, for the particular command above I am getting:
Command 'samtools faidx hg19.fa chr1:115227843-115227863' returned non-zero exit status 127. Am I doing something wrong here?
Just wondering, does samtools itself work when you type samtools? As the manual says, "if a command is not found, the child process created to execute it returns a status of 127" GNU
Yeah samtools does appear to be working fine. I'll try building a new reference and see if this helps.
Maybe your index or fasta are corrupted? Which version of samtools? With samtools 1.3.1: