Hi there I'm trying to follow the instructions here
However when I get to the second step and input:
samtools fixmate -O bam,level=1 -m my.sam fixmate.bam
It tells me that level is an unknown option.
I tried stripping that part of the command so it ran
samtools fixmate -O -m my.sam fixmate.bam
However it just tells me:
Usage: samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam> Options: -r Remove unmapped reads and secondary alignments -p Disable FR proper pair check -c Add template cigar ct tag --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE -O, --output-fmt FORMAT[,OPT[=VAL]]... Specify output format (SAM, BAM, CRAM) --output-fmt-option OPT[=VAL] Specify a single output file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE [null] As elsewhere in samtools, use '-' as the filename for stdin/stdout. The input file must be grouped by read name (e.g. sorted by name). Coordinated sorted input is not accepted.
I tried transposing the -O and -m switches out of desperation but that doesn't run either.
Does anybody perhaps know what I'm doing wrong? Thanks
From what I see, you stripped
-Oalso off the
BAMkeyword, which is required. Might it be only that?
Thanks, I read it defaulted to bam without the keyword but following your advice I tried
It tells me that 'm' is an invalid option.
When I query samtools fixmate /? it says the only options are -r -p -c and -O
I ran samtools --version and it tells me I'm on 1.3.1 which I see is a version from 2016
I'll see if I can get the latest version installed and try again. Thanks.