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Old 05-27-2014, 05:13 AM   #1
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Default BCFTOOLS 0.2 Filter problems

Hi all,
First post here, so I hope I am posting in the right place. I am trying to use BCFTOOLS (version: 0.2.0-rc8-10-g7a1041c) to filter a bcf file but I am running into a couple of problems and I am not sure if I am mis-specifying my filter expressions or if there's a couple of bugs to be ironed out.

UPDATE: I opened this as Issue #51 on the Github page. I will update this if the issue gets updated and vice versa.

e.g. trying to filter based on the genotype filed (FORMAT/GT) I try:

bcftools filter -i 'FORMAT/GT=="1/1"' ./mysnps.bcf | less
I return the bcf header (indicating that bcftools was able to parse the filter expression just fine) but zero variants.

When I also try to use a subscripted FORMAT field (e.g. PL for arguments sake) like this:
bcftools filter -i 'FORMAT/PL[0]==1' ./mysnps.bcf | less
I get the error
Error: Arrays must be subscripted, e.g. PL[0]
Anyone know what I am doing wrong or what is happening? Some filters work just fine, e.g.
bcftools filter -i "%QUAL>30" ./mysnps.bcf | less # this filter works fine
bcftools_0.2 filter -i "FORMAT/SP==1" JEL423.raw.snps.3.bcf | less # using a FORMAT field here works
FYI here are the relevant parts of my bcf header:
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version=3>
##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)">
##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
##bcftools_callCommand=call -vm -O b -

Last edited by simono101; 05-27-2014 at 08:27 AM.
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bcftools, bcftools vcf bcf, bugs, filterexpression

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