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Hi,
I'm having an issue with installing bcftools (mac running Catalina). I used:
`conda install -c bioconda bcftools` (https://anaconda.org/bioconda/bcftools)
However, when I try to call bcftoo…
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iRODS support in Dockerfile below works for the version 1.10.2, but not for 1.11.
```
ARG htsversion=1.10.2
ARG samversion=1.10
ARG bcfversion=1.10.2
```
Specifically, when loading an irods file…
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This seems a really nice tool in exploring QC of vcf. I wanted to give a try. After I installed it in my mac using `pip install vcfstats` and run the example vcf file, I got the error as below. Do yo…
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Hi,
I am getting below error when using plot-vcfstats. I attached the [plot-vcfstats.log](https://github.com/samtools/bcftools/files/39831/plot-vcfstats.txt) for your reference.
Thanks.
I-Hsuan
``…
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Tried `0.6.0` using `pip install -U vcfstats` , but got new error message as below.
$ vcfstats --vcf examples/sample.vcf \
> --outdir examples/ \
> --formula 'COUNT(1) ~ CONTIG' \
> --title '…
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Hey,
I calculated the `bcftools stats -s- vcf_file_chr > chr_stats` for the single chromosomes and plotted the data using `plot-vcfstats -p '' chr_stats` and the result looks ok e.g.
![hwe 0](https…
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since 1.11 at least, I see:
```
gcc -rdynamic -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfann…
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Hello,
we've been using the vxf2sex plugin from the 1.3 version of bcftools successfully for single sample VCF files thus far.
We recently started using this for prediction of gender for a trio VCF …
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I ran plot-vcfstats on a stats file containing this NRD section:
```
# NRD and discordance is calculated as follows:
# m .. number of matches
# x .. number of mismatches
# NRD = (xRR + xR…
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I have a good quality GG/TC MNP:
```
$ freebayes -f /data/reference/ucsc/hg19/hg19.fa -r chr22:42526560..42526563 -F 0.3 reads.bam 2> /dev/null| cut -f1-6 | grep -v "##"
chr22 42526561 . GG …