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Hi there,
I try to filter the ExAC database (.vgf.gz) in Linox Bash shell on windows and get a seg fault after about 5 minutes of running fine.
my input:
bcftools view -i 'FILTER~"PASS"' ExAC.r…
ghost updated
7 years ago
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Dear Jisca,
I am trying to make power analysis on various data quality (mendelian errors and segregation distortions).
My "R loops for" are ok, but as soon as I uncomment sequoia part, the progr…
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I am trying to genotype a sample against a reference VCF file, including homozygous 0/0 calls.
To do this, I first generated a TARGETS file from the reference VCF file which contains the three colu…
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It might be sufficient, especially for SNP calling, to run `PairHMM` over s small number of bases, say 20 or so, surrounding a variant. This might make sense for `HaplotypeCaller` as well. . .
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[angsd-=_shiny_graphing_install_error.txt](https://github.com/mojaveazure/angsd-wrapper/files/1002881/angsd-._shiny_graphing_install_error.txt)
Hi everyone,
Loving all the detailed info provided…
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In our genotyper [BiallelicGenotyper.scala](https://github.com/bigdatagenomics/avocado/blob/master/avocado-core/src/main/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyper.scala#L258) we are p…
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Hello,
I am not able to filter variants based on depth or genotype quality. I used Platypus to call my variants. I saw in already posted issues that this problem is due to Gemini only supporting th…
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This is likely intentional but we should still show these parameters in the #docs.
Test command:
```
WMCF9-CB5:hellbender-protected shlee$ ./gatk-launch Mutect2 -I ~/Documents/workshop_materials…
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samtools mpileup -g -t DP -f hs37d5.fa child.bam father.bam mother.bam -r 9 | dng dnm auto --ped Fam.ped --rd_cutoff 10 --output testFam.vcf --snp_mrate 2e-10 --indel_mrate 1e-11 --bcf -
DeNovoGear…
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Hello,
I am trying to run angsd on two high coverage genomes (size of 57Gb and 83Gb) to estimate genotype likelihoods and get MAFs and beagle files. It's running a few hours and then I got an error m…