Entering edit mode
10.5 years ago
komal.rathi
★
4.1k
Hi everyone (who has used the GSNAP tool for short read alignments),
This is my GSNAP command line:
gsnap -d <genome_file> --gunzip --batch=5 --nthreads=2 --distant-splice-penalty=10000 --clip-overlap -s <splice_file> -N 1 --npaths=100 -Q -v <snp_file> --read-group-id=sample1 --read-group-name=sample1 --read-group-library=sample1 --read-group-platform='Illumina' --format=sam sample1_R1.fastq.gz sample1_R2.fastq.gz 2> sample1.out | samtools view -bS - > sample1.bam
Each time I run this, I get the following errors:
Parse error at line 552039: invalid CIGAR character
sh: line 1: 40402 Broken pipe gsnap -d hg19_gmap --gunzip --batch=5 --nthreads=2 --distant-splice-penalty=10000 --clip-overlap -s Homo_sapiens.GRCh37.72.splicesites.iit -N 1 --npaths=100 -Q -v snp137Common --read-group-id=sample1 --read-group-name=sample1 --read-group-library=sample1 --read-group-platform='Illumina' --format=sam sample1_R1.fastq.gz sample1_R2.fastq.gz 2> sample1.out
40403 Aborted (core dumped) | samtools view -bS - > C01418.bam
Can't figure out what the problem is, Any suggetions?