-
```
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
…
-
Please tag your releases, e.g. `0.1.12b` via `git tag` so they can be referenced here at GitHub. This also allows to use the https://github.com/vcftools/vcftools/releases page.
-
I'm running into this error frequently with SnpEff version SnpEff 4.1l (build 2015-10-03).
```
Error: Error while processing VCF entry (line 10361872) :
13 32893291 rs80358435 G T . . .
…
-
```
❯❯❯ vcftools --version
Error: Unknown option: --version
```
-
Either make vcftools a requirement, or replace these calls with something simpler.
-
It only happens when I use `-m -`, ideas?
```
bcftools norm -f GRCh37.fa -m - test.vcf > test2.vcf
bcftools: vcfnorm.c:385: split_info_numeric: Assertion `ret==src->n_allele-1' failed.
Aborted
```
…
-
The specifications states the following:
> It is strongly encouraged that information lines describing the INFO, FILTER and FORMAT entries used in the body of the VCF file be included in the meta-inf…
-
Yo Kate! Can you do this without removing non-polymorphic SNPs? I think doing so is just a matter of changing this part:
for file in *.gz
do
echo "$file: " $(~/bin/vcftools_0.1.12b/bin/vcfto…
-
Hi Guys,
Im trying to run the test suite but it seems to be falling over at line 360. It seems to be looking for the cavemanVersion header line in the test file which doesn't exist. As a result the c…
-
`
wget https://raw.github.com/chapmanb/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py
python bcbio_nextgen_install.py ~/install/bc --tooldir=~/install/bc-data --genomes hg38 --aligners bwa
`
T…