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Consider the following two variant sites from a VCF:
`#CHROM POS ID REF ALT `
`1 3013782 . A C `
`1 3013783 . C CA `
These sites are on the same haplotype (full vcf lines below). Therefore, th…
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Dear madam/sir,
I have recently tried to use ISOWN, and I was getting a seqmentation fault error when doing the first annotations. I found out that this happens when the software is using qpipeline…
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Table 2 of VCFv4.3.pdf describes the field PL as "Phred-scaled genotype likelihoods rounded to the closest integer", without specifying the tie-breaking rule.
Could you please clarify me whether ties…
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**[Original report](https://bitbucket.org/whatshap/whatshap/issue/159) by Irantzu A (Bitbucket: [iraun](https://bitbucket.org/iraun), ).**
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Hello!
I'm just w…
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Hi.
FORMAT/GT value does NOT match --min-alternate-fraction param?
freebayes version: v1.1.0-22-gf439104
freebayes param:--min-alternate-count 3 --min-alternate-total 6 --min-coverage 10 --min-…
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I'm new to linux and kubernetes so this might be something I'm doing wrong rather than a bug.
Installing seqr on Ubuntu 18.04.1, VM=VirtualBox. All goes fine until deploying seqr pod, then throws fir…
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I recently updated software to samtools/bcftools-1.8 (from v 1.2). After mapping of illumina data to a references (using BWA), I use samtools to call SNPs and bcftools to produce VCF files.
While …
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I just started using DeepVariant 0.7.0 and I have gotten it to complete on a few exome runs. Out of the 4 exome runs I tested, I used 64 shards for the make_examples step. For 3 of the exomes, the m…
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Hello,
I have a set of VCF's that get made into bigquery tables, without error, but aren't working in bigquery.
The resulting schema looks like:
reference_name | STRING | NULLABLE | Referen…
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**[Original report](https://bitbucket.org/whatshap/whatshap/issue/160) by Murray Patterson (Bitbucket: [murraypatterson](https://bitbucket.org/murraypatterson), GitHub: [murraypatterson](https://githu…