Using library htsjdk vcf files

binfoUser · 01-06-2016, 02:32 AM

I want to analyse VCF files that have annotations. I used programs like VEP to annotate the file and now I want to see and manipulate these annotations that are in the file.
I'm using a Java library htsjdk but until now I didn't find any method to manipulate one column (the annotations are added in the INFO column).

Can someone help?

lindenb · 01-06-2016, 05:34 AM

there is currently no automatic method to parse the ouptut of VEP. you need to find the description of the INFO field for VEP from the https://samtools.github.io/htsjdk/ja...VCFHeader.html ( getInfoHeaderLine("CSQ") )

Code:

##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|SYMBOL|SYMBOL_SOURCE|HGNC_ID">

and then, using something like "variantContext.getAttribute("CSQ")" , get the CSQ strings and split the result.

binfoUser · 01-08-2016, 01:45 AM

But the VCFHeader only access the file header and it gives me that line that you showed with id "CSQ". But now I want to extract the info added that is present in the data lines after the header.
I don't understand how to use the "variantContext.getAttribute("CSQ")" that you said. Does that give me that information?

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01-06-2016, 02:32 AM	#1
binfoUser Member Location: Portugal Join Date: Jan 2016 Posts: 22	Using library htsjdk vcf files I want to analyse VCF files that have annotations. I used programs like VEP to annotate the file and now I want to see and manipulate these annotations that are in the file. I'm using a Java library htsjdk but until now I didn't find any method to manipulate one column (the annotations are added in the INFO column). Can someone help?

01-06-2016, 05:34 AM	#2
lindenb Senior Member Location: France Join Date: Apr 2010 Posts: 143	there is currently no automatic method to parse the ouptut of VEP. you need to find the description of the INFO field for VEP from the https://samtools.github.io/htsjdk/ja...VCFHeader.html ( getInfoHeaderLine("CSQ") ) Code: ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele\|Gene\|Feature\|Feature_type\|Consequence\|cDNA_position\|CDS_position\|Protein_position\|Amino_acids\|Codons\|Existing_variation\|DISTANCE\|STRAND\|SYMBOL\|SYMBOL_SOURCE\|HGNC_ID"> and then, using something like "variantContext.getAttribute("CSQ")" , get the CSQ strings and split the result.

01-08-2016, 01:45 AM	#3
binfoUser Member Location: Portugal Join Date: Jan 2016 Posts: 22	But the VCFHeader only access the file header and it gives me that line that you showed with id "CSQ". But now I want to extract the info added that is present in the data lines after the header. I don't understand how to use the "variantContext.getAttribute("CSQ")" that you said. Does that give me that information?