# Streaming gzipped BCF files: issue with CHROM field

**URL:** <https://discourse.julialang.org/t/streaming-gzipped-bcf-files-issue-with-chrom-field/25194>\
**Category:** Biology, Health, and Medicine\
**Created:** [June 12, 2019, 2:59pm UTC](https://discourse.julialang.org/t/streaming-gzipped-bcf-files-issue-with-chrom-field/25194 "2019-06-12T14:59:47Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![kaskarn](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/kaskarn/32/7228_2.png) [@kaskarn](https://discourse.julialang.org/u/kaskarn)\
**Post date:** [June 12, 2019, 2:59pm UTC](https://discourse.julialang.org/t/streaming-gzipped-bcf-files-issue-with-chrom-field/25194/1 "2019-06-12T14:59:47Z")

</div>

Hello,

I first posted this as an issue on the GeneticVariation github:  
[github.com/BioJulia/GeneticVariation.jl/issues/25](http://github.com/BioJulia/GeneticVariation.jl/issues/25)

However, I suspect this may be a better place for it, since the package may not be at fault here. I am copying the issue fuly below; any thoughts would be appreciated!

* * *

Hello,

I am unable to get `BCF.chrom` to output anything other than `1` (Julia 1.1.0; RHEL 7.6).

I tested this with multiple BCF files. When inspected with `bcftools view`, these same files show the correct chromosome name, in the expected field:

```bash
> bcftools view bcftest.bcf.gz
##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype calls">
##FORMAT=<ID=DS,Number=1,Type=Float,Description="Estimated Alternate Allele Dosage : [P(0/1)+2*P(1/1)]">
##contig=<ID=22>
##FORMAT=<ID=GP,Number=3,Type=Float,Description="Genotype call probabilities">
##INFO=<ID=QUAL,Number=1,Type=Float,Description="Imputation Quality">
##INFO=<ID=TAG,Number=1,Type=String,Description="rs_id from annotation files">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##bcftools_viewVersion=1.9+htslib-1.9
##bcftools_viewCommand=view bcftest.bcf.gz; Date=Wed Jun 12 02:41:11 2019
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT XXXX
22 16050075 22:16050075:A:G A G 0.123 PASS TAG=22:16050075:A:G;AC=0;AN=0 GT:DS:GP ./.:0:1,0,0
22 16050115 22:16050115:G:A G A 0.404 PASS TAG=22:16050115:G:A;AC=0;AN=0 GT:DS:GP ./.:0:1,0,0

```

However, `BCF.chrom` tells a different story:

```julia
julia> using GeneticVariation

julia> reader = BCF.Reader(open("bcftest.bcf.gz", "r"))
GeneticVariation.BCF.Reader{IOStream}((0x02, 0x02), GeneticVariation.VCF.Header:
  metainfo tags: fileformat FILTER FORMAT contig INFO
     sample IDs: XXXX, BGZFStreams.BGZFStream{IOStream}(<mode=read>))

julia> record = read(reader)
GeneticVariation.BCF.Record:
   chromosome: 1
     position: 16050075
   identifier: 22:16050075:A:G
    reference: A
    alternate: G
      quality: 0.123
       filter: 1
  information: Tuple{Int64,Any}[(5, "22:16050075:A:G"), (6, 0), (7, 0)]

julia> BCF.chrom(record)
1

julia> BCF.pos(record)
16050075

```

The issue doesn’t seem connected to the actual implementation of `BCF.chrom()`. Reading straight from the `BGZFStream` causes the same issue:

```julia
julia> reader = BCF.Reader(open("bcftest.bcf.gz", "r"))
GeneticVariation.BCF.Reader{IOStream}((0x02, 0x02), GeneticVariation.VCF.Header:
  metainfo tags: fileformat FILTER FORMAT contig INFO
     sample IDs: XXXX, BGZFStreams.BGZFStream{IOStream}(<mode=read>))

julia> misc = read(reader.stream, Int64) #skip first 8 bytes
115964117068

julia> chrom = read(reader.stream, Int32) %Int + 1 #next 4 bytes are CHR
1

julia> pos = read(reader.stream, Int32) %Int + 1 #next 4 bytes are POS
16050075

```

Reproducible example attached: [bcftest.bcf.gz](https://github.com/BioJulia/GeneticVariation.jl/files/3279951/bcftest.bcf.gz)

---

<div class="post-metadata">

**Author:** ![kaskarn](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/kaskarn/32/7228_2.png) [@kaskarn](https://discourse.julialang.org/u/kaskarn)\
**Post date:** [June 12, 2019, 3:55pm UTC](https://discourse.julialang.org/t/streaming-gzipped-bcf-files-issue-with-chrom-field/25194/2 "2019-06-12T15:55:34Z")

</div>

Looks like I should have persevered just a tad longer before posting! In case anyone wonders, the solution can be found in the [VCFv4.3 specs](http://samtools.github.io/hts-specs/VCFv4.3.pdf).

Long story short, (I think) this is an issue with how `GeneticVariation` handles BCF files; instead of storing the explicit chromosome name like in plaintext VCF format, the CHROM field in BCF files stores indices to the list of ‘contig’ field header.

In the example BCF file, there is only one ##contig, with corresponding value `22`. Instead of `1`, `BCF.Chrom` should have returned the value specified by the first ##contig, i.e. `22`.

See page 28 of the specs:

> 6.2.2 Dictionary of contigs  
> The CHROM field in BCF2 is encoded as an integer offset into the list of ##contig field headers in the VCF header. The offsets begin, like the dictionary of strings, at 0. So for example if in BCF2 the contig value is 10, this indicates that the actual chromosome is the 11th element in the ordered list of ##contig elements […]