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fasta sequence does not match the REF allele (again)

1

Hi, I have been trying to generate a consensus sequence using bcftools consensus, but keep failing miserably. The error that i keep getting is: The fasta sequence does not match...

LennWhy

update FILTER col with `annotate` when some variants have multiple flags delimited by ";"

1

I am trying to update the `FILTER` col of a vcf, the possible problem is that some variants have multiple flags delimited with a semicolon annotate.vcf.gz: ``` #CHROM POS ID...

brettva

bcftools reheader -f/--fai does not preserve the order of the contigs (even when it could)

4

I have noticed the following behavior. Suppose I have two files and a reference index: ``` echo -e "##fileformat=VCFv4.2\n##contig=\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\nchr1\t1\t.\tA\tC\t.\t.\t." | bcftools view --no-version -Ob -o chr1.bcf echo -e "##fileformat=VCFv4.2\n##contig=\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\nchr2\t1\t.\tG\tT\t.\t.\t." |...

freeseek

feature request: convert MNPs to SNPs

10

GATK HaplotypeCaller and samtools call these two SNPs at positions i and i+1 (i=763837) for sample NA12878: 20 763837 rs6085879 C T 0/1 20 763838 rs6085880 A G 1/1 In...

tommycarstensen

bcftools mpileup does not use the correct chromosome when using multiple BAM files which have a different chromosome

11

`bcftools mpileup` does not use the correct chromosome when using multiple BAM files which have a different chromosome order. ``` # List of BAM files with BAM files with 2...

ghuls

Allow specification of file type for regions-file

4

I appreciate that `regidx.c` isn't currently up for the task of reading a bcf, but it's more than a little surprising to see that `bcftools merge A.bcf B.bcf -R

CreRecombinase

bcftools norm adding extra variants at the same location with different INFO field values

3

Hello! I used bcftools norm to first split the multi allelic variants and then do left normalization. I noticed that for indels at some locations bcftools norm is adding a...

Ashastry2

1/0 genotype generated by "bcftools norm" at multi-allele sites

2

I ran "bcftools norm" to split multi-allele variants into individual rows. For some of them, 1/0 genotypes were generated. For example, this variant ``` 1 970549 . TGGGG TGG,TGGG,TG,T,GGGGG 1.53856e+06...

weishwu

unresolved sites after using bcftools +fixref

4

Hi, I need to fix the REF allele for my .vcf file per Sanger Imputataion Server's requirement. My .vcf happens to contain dbSNP reference identificators, so I followed the command...

hyl317

Runtime tests are failing on several hardware architectures

12

Hi, the Debian package of bcftools received a [bug report](https://bugs.debian.org/870060) pointing to lots of build time test failures for several architectures. For instance you can check a [log of a...

tillea