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Hi Thomas,
I'm trying to use .bams from 10x genomics with HipSTR. It looks like all reads are getting filtered out. for example when I run against your precompiled .bed file all the entries look like…
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Hi,
When I try to import a vcf file into the database by using the vcf2tiledb command I got the following error:
[E::vcf_hdr_read_requierd_sample_line] No sample line
Do you have any recommenda…
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Hi,
I am trying to write some code to convert VCF to QCALL format, because I need to use QCALL as input for a specific software. I have a few old QCALL and VCF files from low-coverage samples I am us…
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Hi, I have a somatic mutation filtered VCF file generated by GATK haplotypeCaller. I used that file to run MuPeXI on the web server, but got the following errors. Could you please let me know what's w…
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To get an unbiased evaluation of libprosic-based calling of single nucleotide variant `Event`s, these should not only be called where the candidates provide a possible alternative allele, but also at …
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@davidbenjamin commented on [Thu Feb 16 2017](https://github.com/broadinstitute/gatk-protected/issues/909)
It might be sufficient, especially for SNP calling, to run `PairHMM` over s small number of …
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Hi!
I hope this is not due to my file but when testing `vt sort` on a toy example with `-m full` (default option), I didn't get what is expected. If I try the tool `vcf-sort` on the same file, the …
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Hello,
I apply pcangsd in genotype likelihoods in Beagle format (from angsd), and get the results with suffix include .cov .inbreed .indmafs.gz .mafs.gz .selection.gz. But I can not find th…
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Hi, vep team.
I have a vcf file, and annotate it using vep release/90. I want to filter the AF to find mutations whose value below 0.05. My cmd is `filter_vep -i test_annos.vcf/test_annos.tsv -filter…
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```
Write out vds: gs://seqr-hail/datasets/GRCh38/1kg/1kg.liftover.vep.vds
[Stage 5:======================================================> (22 + 1) / 23]Traceback (most recent call last):
File …