bcftools: DP filter based on chromosome and sex

Question

[bsmith030465]

Hi,

I want to filter my bcf file such that:

1. Autosomal chromosomes are filtered with DP > 20
2. X chromosome, for females is filtered with DP > 20
3. X chromosome, for males, with DP > 10 (i.e relax this criteria for males)

My current plan is to split the data into autosomal (and chrY) and X chromosome using something like (any way to specify chr1-chr22?):

bcftools view -i 'DP>20' input.bcf --regions chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrY -Ob -o autosomalY.bcf


## sample ids as they appear in input.bcf file
bcftools query -l input.bcf > allsampleids.txt

I can process the X chromosome using:

## assuming femaleIDs.txt contains female sample ids
bcftools view -i 'DP>20' input.bcf --regions chrX --samples-file femaleIDs.txt -Ob -o Xfemales.bcf
bcftools view -i 'DP>10' input.bcf --regions chrX --samples-file ^femaleIDs.txt -Ob -o Xmales.bcf

My questions:

1. How should I recombine the outputs, such that I again have one bcf dataset? i.e. how do I combine autosomalY.bcf, Xfemales.bcf and Xmales.bcf? Not sure if this is possible or even a good idea....
2. Is there a cleaner way to do this?

Thanks!

Answer 1

[Pierre Lindenbaum]

using vcffilterjdk

with the code:

if(variant.getContig().equals("Y")) {
    return false;
    }
else if(variant.getContig().equals("X")) {
final Set<String> setM = CollectionUtil.makeSet("S1","S2");
final Set<String> setF = CollectionUtil.makeSet("S2","S4","S5");

boolean ok_m = variant.getGenotypes().stream().filter(G->G.hasDP() && setM.contains(G.getSampleName())).mapToInt(G->G.getDP()).sum() > 10;
boolean ok_f = variant.getGenotypes().stream().filter(G->G.hasDP() && setF.contains(G.getSampleName())).mapToInt(G->G.getDP()).sum() > 20;

return ok_m && ok_f;
}
else
{
return variant.getAttributeAsInt("DP",0)>20;
}

exemple:

java -jar dist/vcffilterjdk.jar -f input.code input.vcf

[bsmith030465]

Hi Pierre,

Thanks!!!

It would be extremely helpful if there was some documentation with this (where is it reading the male/female ids?). Also, what if I wanted to to do 'DP>10 & GQ >10', how do I incorporate multiple conditions?

[Pierre Lindenbaum]

t would be extremely helpful if there was some documentation

my bad ! I forgot to add the link : http://lindenb.github.io/jvarkit/VcfFilterJdk.html

where is it reading the male/female ids

it's hard coded:

final Set<String> setM = CollectionUtil.makeSet("S1","S2");

how do I incorporate multiple conditions?

basically it requires to a knowledge of java and the library for HTS. But there are many examples or links to previous biostar post in the manual : http://lindenb.github.io/jvarkit/VcfFilterJdk.html