About structure variants simulation

Question

[Darren Lin]

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?

[Kevin Blighe]

Output the lines before and after chr1, 788889