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Hi Tamsen,
I run the following command:
/pisces_all/Pisces -bam /my/my.bam -g /HUMAN/FASTA/ -o /my/out
and got a very big VCF file (~10GB) with, I guess, all covered positions (first lines below)…
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Hello,
Sorry me again! I was just wondering if a bed file is required for every WES analysis? I've ran deepvariant without adding one, but think I should have included one? Would I get this WES be…
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Hello,
I try to use bcftools norm with the command :
```
bcftools view --threads 6 \
-f .,PASS \
${TMP_DIR}/${VCF} \
--regions-file ${interval} \
| \
bcftools norm \
-m - -w 10000 -f ${…
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Apparently the index of deduped and recalibrated BAMs are mixed up:
```
szilva@munin /data2/GMS_test/BTB0001 $ nextflow pull nf-core/sarek -r dev
Checking nf-core/sarek ...
Already-up-to-date -…
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This might be an obvious question but i cannot work it out, what does the -B mean?
For example from your singularity guide:
```
singularity run **-B** /usr/lib/locale/:/usr/lib/locale/ \
do…
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Hey Luc
as,
I was just wondering, is there a possibility to get as an output of grenepipe a vcf file just like the variance file, but not only with the variances, but with all the information on rea…
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https://mp.weixin.qq.com/s/E_r04XQvYZfKrJ0_KFf7_Q
ixxmu updated
2 years ago
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Hello,
I ran into a strange difference in output between gVCF and VCF runs of the same samples and was hoping to get some input into how it happens.
Background: I've been using [strelka2](http…
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I ran DeepVariant(r1.1.0) and merged 1305 gvcfs by GLnexus (WES data).
I found one important site:
- QUAL(the 6th column) 25
- AQ(the 8th column) 25
- the genotype of 4 samples(controls and case…
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I am interested on calling variants from a bam file and a reference genome in a diploid organism.
I installed medaka using miniconda (`conda create -n medaka -c conda-forge -c bioconda medaka`)
…