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From: Francesco L. <f.l...@uc...> - 2011-05-26 15:50:18
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I am trying to merge two vcf containing multiple samples but the process gives continuosly this error Use of uninitialized value in hash element at /share/apps/genomics/vcftools-0.1.4a/perl/Vcf.pm line 498, <$__ANONIO__> line 6. Use of uninitialized value in hash element at /share/apps/genomics/vcftools-0.1.4a/perl/Vcf.pm line 498, <$__ANONIO__> line 6. and the resulting file appears like that 1 13438 . CTT C 167.00 PASS AC=1;AN=344;DP=110;HP=4;NF=3;NFS=23;NR=7;NRS=37;SF=1 GT:GQ . . . . .Use of uninitialized value in hash element at /share/apps/genomics/vcftools-0.1.4a/perl/Vcf.pm line 498, <$__ANONIO__> line 6. Use of uninitialized value in hash element at /share/apps/genomics/vcftools-0.1.4a/perl/Vcf.pm line 498, <$__ANONIO__> line 6. Use of uninitialized value in hash element at /share/apps/genomics/vcftools-0.1.4a/perl/Vcf.pm line 498, <$__ANONIO__> line 6. 1 1115555 . C CT 40.00 PASS AC=1;AN=344;DP=12;HP=1;NF=1;NFS=3;NR=1;NRS=2;SF=1 GT:GQ . . . . 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0: 0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/1:40 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0: 0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0:0 0/0Use of uninitialized value in hash element at /share/apps/genomic s/vcftools-0.1.4a/perl/Vcf.pm line 498, <$__ANONIO__> line 50. Use of uninitialized value in hash element at /share/apps/genomics/vcftools-0.1.4a/perl/Vcf.pm line 498, <$__ANONIO__> line 50. I also had to clean the file from messages like "Using colum name 'UCL.._data" which should be a STDERR but appear to be directed into the file I tried the same using just one sample, using vcf-concat on the snps and the indel files, but it doesn't accept it since it says the colums have different names (one has been converted from 3.3 samtools to 4.0 with the vcf-convert tool, the other has been produced by dindel. thanks for your help, Francesco -- |