Filtering info column

Question

[taijc06]

Hi all,

I have a vcf file with an info column like this:

##fileformat=VCFv4.3
##fileDate=20180421
##source=PLINKv2.00
##filedate=20180410
##contig=<ID=10,length=135524727>
##INFO= ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|REFSEQ_MATCH|SOURCE|GENE_PHENO|SIFT|PolyPhen|DOMAINS|miRNA|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_A F|AA_AF|EA_AF|gnomAD_AF|gnomAD_AFR_AF|gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|gnomAD_NFE_AF|gnomAD_OTH_AF|gnomAD_SAS_AF|MAX_AF|MAX_AF_POPS|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE"
#CHROM  POS     ID      REF     ALT

I would like to only obtain the allele frequency (AF) data from the column. However, it is quite difficult for me to do so as all the data are clustered as one column. Are there any ways for me to overcome this? Thank you

Answer 1

[NB]

Hello, You can use bcftools to extract AF info. The command is something like this

bcftools query -f '%CHROM %POS %AF\n' input.vcf> ouput.vcf

You can read the manual for more info, incase AF tag is not present in your vcf INFO

[Pierre Lindenbaum]

OP wants the information that is contained into the VEP INFO/CSQ field, not the INFO/AF

[NB]

Sorry misunderstood the question, ignore my answer... not sure then... maybe generate the VEP output in a tab format to avoid the clustering and then extract the AF column.

Answer 2

[Pierre Lindenbaum]

using bioalcidaejdk : http://lindenb.github.io/jvarkit/BioAlcidaeJdk.html

the code contains a variable 'tools' which itself contains a parser for the VEP output. There are some duplicated lines if there is more than one transcript per variant.

 java -jar dist/bioalcidaejdk.jar -e 'println("CHROM\tPOS\tREF\tAF");stream().forEach(V->tools.getVepPredictions(V).stream().forEach(P->{println(V.getContig()+"\t"+V.getStart()+"\t"+V.getReference().getDisplayString()+"\t"+P.getByCol("AF"));}));'

CHROM   POS REF AF
21  26960070    G   0.0014
21  26960070    G   0.0014
21  26960070    G   0.0014
21  26965148    G   0.7324
21  26965148    G   0.7324
21  26965148    G   0.7324
21  26965172    T   0.0106
21  26965172    T   0.0106
21  26965172    T   0.0106
21  26965205    T   0.7324
21  26965205    T   0.7324
21  26965205    T   0.7324
21  26976144    A   0.0004
21  26976144    A   0.0004
21  26976144    A   0.0004
(...)