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Old 12-07-2012, 12:36 PM   #24
rama
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Location: Boston, USA

Join Date: Jan 2011
Posts: 20
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Laura,

I tried with downloading both the vcf.gz and tbi files. but it did not work and it is difficult to interpret the error. can you see what I am doing wrong here

./tabix -h /Volumes/Macintosh\ HD\ 3/1000Genome/ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites.vcf.gz | perl ~/othertools/vcftools_0.1.10/perl/vcf-subset -c NA10851

[tabix] the index file exists. Please use '-f' to overwrite.
Broken VCF header, no column names?
at /Users/molpathuser1/othertools/vcftools_0.1.10/perl//Vcf.pm line 177
Vcf::throw('Vcf4_1=HASH(0x7fa9d982f8d8)', 'Broken VCF header, no column names?') called at /Users/molpathuser1/othertools/vcftools_0.1.10/perl//Vcf.pm line 869
VcfReader::_read_column_names('Vcf4_1=HASH(0x7fa9d982f8d8)') called at /Users/molpathuser1/othertools/vcftools_0.1.10/perl//Vcf.pm line 604
VcfReader:arse_header('Vcf4_1=HASH(0x7fa9d982f8d8)') called at /Users/molpathuser1/othertools/vcftools_0.1.10/perl/vcf-subset line 122
main::vcf_subset('HASH(0x7fa9d98288f0)') called at /Users/molpathuser1/othertools/vcftools_0.1.10/perl/vcf-subset line 12

many thanks for your kind help
rama is offline   Reply With Quote