This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Preparing a appropriate VCF in order to support my Implementation

I have section called Variant Call Data section, When User views the Variant Call Data section,Then those values should be extracted from the called variant VCF.

My VCF contains

#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    sample

But I want to include GATK, Read Depth and Zygosity information as well.How should I approach to this

Any help?

snp ngs vcf
• 3,054 views • link
updated by Ram Ram • written by gaurav.singh • gaurav.singh

At least some of the information you want is in the VCF file, so just parse the file and include it.

• 0 views • link
written by Devon Ryan Devon Ryan

Then you'll need to determine them. This may require the original data.

• 0 views • link
written by Devon Ryan Devon Ryan

I can not just manually added to it right?

• 0 views • link
written by gaurav.singh • gaurav.singh

If you've calculated the values then sure, you can add them. Just keep it in VCF format.

• 0 views • link
written by Devon Ryan Devon Ryan

define "my implementation"

you only show a standard VCF header. show a larger sample (headers & variants)

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum 
#reference=file:///usr/local/mrgstorage/files/deployment_package/d1/refseq/build.hg19/hg19.fasta                                    
#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    sample
chr4    55524065    .    G    A    100    PASS    TC=SUB1;DP=100;FS=2.000;HRun=2;Gene=KIT    GT:AD:DP:GQ:PL    0/1:334,288:100:99:7146,0,8593
chr4    55524133    .    C    T    100    PASS    TC=SUB2;DP=100;FS=2.000;HRun=2;Gene=KIT    GT:AD:DP:GQ:PL    0/1:334,288:100:99:7146,0,8593
chr4    55524211    .    T    C    100    PASS    TC=SUB3;DP=100;FS=2.000;HRun=2;Gene=KIT    GT:AD:DP:GQ:PL    0/1:334,288:100:99:7146,0,8593
chr4    55524205    .    G    C    100    PASS    TC=SUB4;DP=100;FS=2.000;HRun=2;Gene=KIT    GT:AD:DP:GQ:PL    0/1:334,288:100:99:7146,0,8593
chr4    55524217    .    C    A    100    PASS    TC=SUB5;DP=100;FS=2.000;HRun=2;Gene=KIT    GT:AD:DP:GQ:PL    0/1:334,288:100:99:7146,0,8593
chr4    55569979    .    T    C    100    PASS    TC=SUB6;DP=100;FS=2.000;HRun=2;Gene=KIT    GT:AD:DP:GQ:PL    0/1:334,288:100:99:7146,0,8593
chr4    55569909    .    A    C    100    PASS    TC=SUB7;DP=100;FS=2.000;HRun=2;Gene=KIT    GT:AD:DP:GQ:PL    0/1:334,288:100:99:7146,0,8593
chr4    55569919    .    G    A    100    PASS    TC=SUB8;DP=100;FS=2.000;HRun=2;Gene=KIT    GT:AD:DP:GQ:PL    0/1:334,288:100:99:7146,0,8593
chr4    55604609    .    A    G    100    PASS    TC=SUB9;DP=100;FS=2.000;HRun=2;Gene=KIT    GT:AD:DP:GQ:PL    0/1:334,288:100:99:7146,0,8593
chr4    55604637    .    C    A    100    PASS    TC=SUB10;DP=100;FS=2.000;HRun=2;Gene=KIT    GT:AD:DP:GQ:PL    0/1:334,288:100:99:7146,0,8593
chr4    55604618    .    C    A    100    PASS    TC=SUB11;DP=100;FS=2.000;HRun=2;Gene=KIT    GT:AD:DP:GQ:PL    0/1:334,288:100:99:7146,0,8593
chr4    55604784    .    G    A    100    PASS    TC=SUB12;DP=100;FS=2.000;HRun=2;Gene=KIT    GT:AD:DP:GQ:PL    0/1:334,288:100:99:7146,0,8593
chr4    55549723    .    C    G    100    PASS    TC=SUB13;DP=100;FS=2.000;HRun=2;Gene=KIT    GT:AD:DP:GQ:PL    0/1:334,288:100:99:7146,0,8593
chr4    55598008    .    T    A    100    PASS    TC=SUB14;DP=100;FS=2.000;HRun=2;Gene=KIT    GT:AD:DP:GQ:PL    0/1:334,288:100:99:7146,0,8593
chr4    55604087    .    C    A    100    PASS    TC=SUB15;DP=100;FS=2.000;HRun=2;Gene=KIT    GT:AD:DP:GQ:PL    0/1:334,288:100:99:7146,0,8593
chr4    55524249    .    G    A    100    PASS    TC=SUB16;DP=100;FS=2.000;HRun=2;Gene=KIT    GT:AD:DP:GQ:PL    0/1:334,288:100:99:7146,0,8593
chr4    55524250    .    T    C    100    PASS    TC=SUB17;DP=100;FS=2.000;HRun=2;Gene=KIT    GT:AD:DP:GQ:PL    0/1:334,288:100:99:7146,0,8593
chr4    55561676    .    A    T    100    PASS    TC=SUB18;DP=100;FS=2.000;HRun=2;Gene=KIT    GT:AD:DP:GQ:PL    0/1:334,288:100:99:7146,0,8593
• 0 views • link
updated by Ram Ram • written by gaurav.singh • gaurav.singh

0 answers

No answers yet.

Log in to answer this question.

More posts like this