hi, i'm learning the CONTRA, by using the test datas downloaded on sourceforge, command as follows { Python-2.7/python CONTRA.v2.0.3/contra.py -t 0247401_D_BED_20090724_hg19_MERGED.bed -s P0667T_GATKrealigned_duplicates_marked.bam -c P0667N_GATKrealigned_duplicates_marked.bam -f human.fa -o outdir };
here are the programs in it:
1. Python-2.7
2. R version 2.10.0
3. samtools version: 0.1.8
4. BEDTools-Version-2.11.2
No error reports during processing(just like the web shows http://sourceforge.net/projects/cont.../Test%20files/). 3 files in the '/outdir/table' dir (CNATable.10rd.10bases.20bins.vcf; CNATable.10rd.10bases.20bins.DetailsFILTERED.txt; CNATable.10rd.10bases.20bins.txt), there are no cnv information in vcf file, only this description (
##fileformat=VCFv4.0
##reference=1000GenomesPilot-NCBI36
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"
##ALT=<ID=CNV,Description="Copy number variable region"
#CHROM POS ID REF ALT QUAL FILTER INFO)
dose anyone know why?? thanks for help~
here are the programs in it:
1. Python-2.7
2. R version 2.10.0
3. samtools version: 0.1.8
4. BEDTools-Version-2.11.2
No error reports during processing(just like the web shows http://sourceforge.net/projects/cont.../Test%20files/). 3 files in the '/outdir/table' dir (CNATable.10rd.10bases.20bins.vcf; CNATable.10rd.10bases.20bins.DetailsFILTERED.txt; CNATable.10rd.10bases.20bins.txt), there are no cnv information in vcf file, only this description (
##fileformat=VCFv4.0
##reference=1000GenomesPilot-NCBI36
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"
##ALT=<ID=CNV,Description="Copy number variable region"
#CHROM POS ID REF ALT QUAL FILTER INFO)
dose anyone know why?? thanks for help~
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