Question: Preparing a appropriate VCF in order to support my Implementation
0
gravatar for gaurav.singh
4.9 years ago by
gaurav.singh10
United States
gaurav.singh10 wrote:

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 shoud I approach to this

Any help?

 

 

snp ngs vcf • 1.3k views
ADD COMMENTlink modified 4.9 years ago by Pierre Lindenbaum126k • written 4.9 years ago by gaurav.singh10

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

ADD REPLYlink written 4.9 years ago by Devon Ryan94k

But my vcf do not have these values?

ADD REPLYlink written 4.9 years ago by gaurav.singh10

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

ADD REPLYlink written 4.9 years ago by Devon Ryan94k

I can not just manually added to it right?

ADD REPLYlink written 4.9 years ago by gaurav.singh10

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

ADD REPLYlink written 4.9 years ago by Devon Ryan94k

define "my implementation"

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

ADD REPLYlink written 4.9 years ago by Pierre Lindenbaum126k

#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

ADD REPLYlink written 4.9 years ago by gaurav.singh10
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