bcftools

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Feature request: the inverse of `norm --atomize`

1

I found normalization will give incorrect result in this case: ``` 1 | a1 ACGCTCCTCC TCCAGA a2 -------*** ------ a3 ---*------ ------ a4 ---*---*** ------ ``` ``` sh-5.0# bcftools view...

linnil1

bcftools fails to genotype MNP/indels from targeted-sequencing reads

4

Hi, Given a list of known alleles, I was trying to genotype REF/ALT read counts in some samples' BAM files. Relevant to the issue below is that these are libraries...

haochenz96

Fix vcf-merge when using COLLAPSE_NONE

1

Fix vcf-merge when using COLLAPSE_NONE: Only perfect-match triggers the merge event.

starskyzheng

bcftools can not call low allele frequency

5

Hello there, I'm doing some SNP calling with samtools mpileup -Q 0 -uvf | bcftools -vm -Oz but after running the pipeline, I noticed that all my SNPs are with...

YS-HZAU

Too many alleles (>32) at chr1:24859772, skipping. (todo?)

2

what does that mean? this site chr1:24859772 has too many variation?

hanguojun007

Regions file parsing broken

7

$ bcftools --version bcftools 1.10.2 Using htslib 1.10.2 Copyright (C) 2019 Genome Research Ltd. $ cat regions_test.txt NC_000001.11 1 $ cat -A regions_test.txt NC_000001.11^I1$ $ bcftools view -H -R regions_test.txt...

bamyasi

Improvements to indel calling.

6

- The bcf_call_glfgen code had a heuristic to change indel type calls to 0 (REF) where the read doesn't have an indel at that location, under the assumption our assessment...

jkbonfield

Make --indel-bias more sensitive to indels

4

by switching off an existing heuristics which reduces indelQ and, in the extreme case, has the power to discard an indel entirely when the reference alignment has low score. This...

pd3

pd3

mcshane