Raheleh

Dear Dan, many thanks for your reply. How can I merge my vcf files? I tried to use CombineVariants to combine my 6 vcf files, but I get this error : Unable to access jarfile/ GenomeAnalysisTK.jar In fact there is no file namely GenomeAnalysisTK.jar. Do you know how can I fix this problem? Another problem is about the format of vcf file, it's not the same as accepted format for ANNOVAR. How can I convert them to annovar format? About the vcf file could you please tell me why the third colum (ID) is...

Dear Dan, many thanks for your reply. How can I merge my vcf files? I tried to use CombineVariants to combine my 6 vcf files, but I get this error : Unable to access jarfile/ GenomeAnalysisTK.jar In fact there is no file namely GenomeAnalysisTK.jar. Do you know how can I fix this problem? Another problem is about the format of vcf file, it's not the same as accepted format for ANNOVAR. How can I convert them to annovar format? About the vcf file could you please tell me why the third colum (ID) is...

Hello, I am sorry for the very basic question but I am confusing and getting lost in my thoughts. I have WES data of tumor samples with matched ones extracted from 13 patients (paired-end, illumina). I used BWA mem to align them against hg38, and used VarScan2 to call somatic variations. Now I have 6 files (fpfilter_Passed.vcf) for each patient (Somatic, LOH, Germline for each of snp and indel variations). My question is, what I have to do in this step? Should I merge all 6 files together? If so,...

The problem solved! It was becaucas of my input file. instead of vcf file I was giving var file (all.Somatic.hc.var) to fpfilter.

Hello, I am new in field of NGS analysis. I have 76 WES data from tumor samples along with matched ones (paired-end, illumina) to find somatic and germline variations. I used VarScan fpfilter for 3 .hc.vcf files (somatic, germline, LOH) to filter false positives, but it returned this: Use of uninitialized value $var in uc at variant-filter-master/fpfilter.pl line 128, <GEN2> line 882. Use of uninitialized value $var in uc at variant-filter-master/fpfilter.pl line 128, <GEN2> line 883. Use of uninitialized...

Hello, I am new in field of NGS analysis. I have 76 WES data from tumor samples along with matched ones (paired-end, illumina) to find somatic and germline variations. I used VarScan fpfilter for 3 .hc.vcf files (somatic, germline, LOH) to filter false positives, but it returned this: Use of uninitialized value $var in uc at variant-filter-master/fpfilter.pl line 128, <gen2> line 882. Use of uninitialized value $var in uc at variant-filter-master/fpfilter.pl line 128, <gen2> line 883. Use of uninitialized...