I've just started using bcftools stats, so I still don't know much, but for me, I get an error when I don't give a bgzip compressed file, could that be your case? You can get the bgzip in the htslib package, after that, you need to index the bgzip file with bcftools index. Do you think that would help?
By the way, just getting a ride on your question, does anyone know where to find the documentation for the bcftools stats output? I've got some weird results that I would like to understand better. I've asked the same question here: http://seqanswers.com/forums/showthread.php?t=57687
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VCFtools error
Originally posted by yl01 View PostIt looks like the vcftools you are using is of version 0.1.4a. So the first thing i would try is to install the updated version, which is 0.1.11.
Use of uninitialized value $attr_value in pattern match (m//) at /home/../vcftools_0.1.11/perl/Vcf.pm line 2971, <__ANONIO__> line 6.
at /home/bliu1/vcftools_0.1.11/perl/Vcf.pm line 2971.
Could you help? thanks
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It looks like the vcftools you are using is of version 0.1.4a. So the first thing i would try is to install the updated version, which is 0.1.11.
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Error using vcf-stats
I am trying to figure out the variant statistics from a vcf file using the command:
Code:./vcf-stats NA11881roi_variants.vcf
Code:The version "4.1" not supported, assuming VCFv4.0 Expected GT as the first genotype field at chr4:46036725 Use of uninitialized value $gtype in pattern match (m//) at /N/dc/scratch/bansalr/bowtie2-2.1.0/vcftools_0.1.4a/perl/Vcf.pm line 1060, <__ANONIO__> line 28. Use of uninitialized value $gtype in concatenation (.) or string at /N/dc/scratch/bansalr/bowtie2-2.1.0/vcftools_0.1.4a/perl/Vcf.pm line 1060, <__ANONIO__> line 28. Could not parse gtype string [] at /N/dc/scratch/bansalr/bowtie2-2.1.0/vcftools_0.1.4a/perl/Vcf.pm line 167, <__ANONIO__> line 28. Vcf::throw('Vcf4_0=HASH(0x260f630)', 'Could not parse gtype string []\x{a}') called at /N/dc/scratch/bansalr/bowtie2-2.1.0/vcftools_0.1.4a/perl/Vcf.pm line 1060 VcfReader::parse_alleles('Vcf4_0=HASH(0x260f630)', 'HASH(0x25221d8)', 'NA11881roi.sorted.bam') called at ./vcf-stats line 83 main::vcf_stats('HASH(0x2237de8)') called at ./vcf-stats line 9
Thank you!
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