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after running all the three step got the windows1.glf.txt and windows2.glf.txt
i have copy the path of these files in one file ie. glf.txt
/home/dindel/windows1.glf.txt
/home/dindel/windows2.glf.txt
and run the ./mergeOutputDiploid.py --inputfile glf.txt --outputFile var.VCF --ref hg18.fa
but the VCF file is empty
can any body figure out why i am getting blank VCF file
##fileformat=VCFv4.0
##source=Dindel
##reference=/home/pankajv/Tools/chr10_PTEN/89623195_89728532_head.fasta
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total number of reads in haplotype window">
##INFO=<ID=HP,Number=1,Type=Integer,Description="Reference homopolymer tract length">
##INFO=<ID=NF,Number=1,Type=Integer,Description="Number of reads covering non-ref variant on forward strand">
##INFO=<ID=NR,Number=1,Type=Integer,Description="Number of reads covering non-ref variant on reverse strand">
##INFO=<ID=NFS,Number=1,Type=Integer,Description="Number of reads covering non-ref variant site on forward strand">
##INFO=<ID=NRS,Number=1,Type=Integer,Description="Number of reads covering non-ref variant site on reverse strand">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
##ALT=<ID=DEL,Description="Deletion">
##FILTER=<ID=q20,Description="Quality below 20">
##FILTER=<ID=hp10,Description="Reference homopolymer length was longer than 10">
##FILTER=<ID=fr0,Description="Non-ref allele is not covered by at least one read on both strands">
##FILTER=<ID=wv,Description="Other indel in window had higher likelihood">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
Thanks
i have copy the path of these files in one file ie. glf.txt
/home/dindel/windows1.glf.txt
/home/dindel/windows2.glf.txt
and run the ./mergeOutputDiploid.py --inputfile glf.txt --outputFile var.VCF --ref hg18.fa
but the VCF file is empty
can any body figure out why i am getting blank VCF file
##fileformat=VCFv4.0
##source=Dindel
##reference=/home/pankajv/Tools/chr10_PTEN/89623195_89728532_head.fasta
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total number of reads in haplotype window">
##INFO=<ID=HP,Number=1,Type=Integer,Description="Reference homopolymer tract length">
##INFO=<ID=NF,Number=1,Type=Integer,Description="Number of reads covering non-ref variant on forward strand">
##INFO=<ID=NR,Number=1,Type=Integer,Description="Number of reads covering non-ref variant on reverse strand">
##INFO=<ID=NFS,Number=1,Type=Integer,Description="Number of reads covering non-ref variant site on forward strand">
##INFO=<ID=NRS,Number=1,Type=Integer,Description="Number of reads covering non-ref variant site on reverse strand">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
##ALT=<ID=DEL,Description="Deletion">
##FILTER=<ID=q20,Description="Quality below 20">
##FILTER=<ID=hp10,Description="Reference homopolymer length was longer than 10">
##FILTER=<ID=fr0,Description="Non-ref allele is not covered by at least one read on both strands">
##FILTER=<ID=wv,Description="Other indel in window had higher likelihood">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
Thanks
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