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:
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:
I get the error
Anyone know what I am doing wrong or what is happening? Some filters work just fine, e.g.
FYI here are the relevant parts of my bcf header:
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:
Code:
bcftools filter -i 'FORMAT/GT=="1/1"' ./mysnps.bcf | less
When I also try to use a subscripted FORMAT field (e.g. PL for arguments sake) like this:
Code:
bcftools filter -i 'FORMAT/PL[0]==1' ./mysnps.bcf | less
Code:
Error: Arrays must be subscripted, e.g. PL[0]
Code:
bcftools filter -i "%QUAL>30" ./mysnps.bcf | less [COLOR="Silver"][I]# this filter works fine[/I][/COLOR] bcftools_0.2 filter -i "FORMAT/SP==1" JEL423.raw.snps.3.bcf | less [COLOR="Silver"][I]# using a FORMAT field here works[/I][/COLOR]
Code:
##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"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##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_callVersion=0.2.0-rc8-10-g7a1041c+htslib-0.2.0-rc8-6-gd49dfa6 ##bcftools_callCommand=call -vm -O b - ##bcftools_viewVersion=0.2.0-rc8-10-g7a1041c+htslib-0.2.0-rc8-6-gd49dfa6