Entering edit mode
6.4 years ago
Darren Lin
•
0
Guys, I am trying to use DWGSIM to generate some simulation paired-end reads with a VCF file of candidate mutations. I use the command like : dwgsim -1 101 -2 101 -v true.vcf ucsc.hg19.fasta read
But it gives an error message "out of order [chr1, 788889]". The error message indicates this line in the VCF: chr1 788889 . C T 20 PASS . GT 1|1
My VCF looks like this, and can be found at http://smash.cs.berkeley.edu/datasets.html
##fileformat=VCFv4.0
##source=VCFWriter
##INFO=<ID=OP,Number=1,Type=Integer,Description="Original position before normalization">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
chr1 65745 . A G 20 PASS . GT 1|1
chr1 65797 . T C 20 PASS . GT 1|1
chr1 65872 . T G 20 PASS . GT 1|1
Are there any suggestions for this?
Output the lines before and after
chr1, 788889