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Hi Brad,
I found the following new multiple errors by using the same tumor-normal pipeline that I kept running successfully recently. In the slurm file, I used --retries 3 option. Could you please hel…
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http://sourceforge.net/projects/vcftools/files/
oguya updated
9 years ago
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The following extension to BCF has been agreed on the vcftools-spec mailling list which introduces end-of-vector byte to allow missing values in vectors. This is the proposed text which will appear in…
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Can you point me to BAMTools v1.1? I think this is related to #31
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Since we are calling variants we should consider adding support to generate VCF files for each method in addition the BED files.
- see VCF format specification here: http://vcftools.sourceforge.net/sp…
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The ability to select a sample by name to perform bed operations on. This would help with using vcf files from the 1000 genomes project where we are trying to intersect with certain individuals.
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VCF should either have an option in the header to choose a specific string encoding (e.g: utf-8, latin-1, ascii) with a default option set, or it should be documented which encoding VCF should be in.
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```
When outputting insertions, gdtools GD2VCF will output the location of the
previous base. VCFTools seems to expect the position after (where the insertion
goes). Specifically, when running vcf-c…
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```
What steps will reproduce the problem?
1. Create a VCF file a.vcf with this line:
20 1711570 . T TG 59 PASS
DP=173;NF=0;NR=0;NRS=5;NFS=3;HP=1 GT:GQ 0/1:20
…