Hi all

I called six SNP's files as individual, I want to merge them such that considering the position and location. I want to do that for converting them as integer numbers 0,1,2.

The question is:

Could anyone please help me how I can merge them as following?

REF is hg19 , ALT1 is first patient, ALT2 second patient ... so on till ALT6 sixth patient.

```
#CHROM   POS     REF   ALT1   ALT2   ALT3   ALT4   ALT5   ALT6
chrM     3       T     C      G      A      C      T      C
chrM     4       C     A      C      T      A      G      C
chrM     150     T     C      T      C      C      G      A
chrM     195     C     T      C      T      C      A      T
chrM     410     A     T      T      C      C      T      C
chrM     711     G     A      C      T      T      G      G
chrM     1890    G     .      C      T      C      A      C
chrM     2354    C     T      T      C      A      G      C
chrM     2485    C     T      A      G      G      A      C,T
chrM     3457    T     C      G      A      G      A      C
chrM     4162    C     T      T      A      T      C,A    A
chrM     4217    T     C      G      T      A      G      T
chrM     4918    A     G      C      .      G      A      A
chrM     5581    C     T      G      A      A      G      .
chrM     8698    G     A      G      A      A      C      A
chrM     8702    G     A      G      C      G      C      A
chrM     9378    G     A      C      T      G      A      C
chrM     9541    C     T      C      T      C      T      C
chrM     10284   A     G      G      A      A      C      C
chrM     10399   G     A      G      A      A      G      T
chrM     10464   T     C      C      G      T      C      G
chrM     10820   G     A      G      T      .      C      A
chrM     10874   C     T      G      T      G      C,T    G
chrM     11018   C     T      C      T      A      C      C
chrM     11252   A     G      .      C      G      A      T
chrM     11723   C     T      .      A      C      T      T
chrM     11813   A     G      G      A      C      A      C
```

Is that possible? I wrote period because someone told me you should have these periods if the positions there!

Thank you in advance

Bing
Assuming you have 6 VCF files, you can use GATK.

    java -jar GenomeAnalysisTK.jar \
    -T CombineVariants \
    -R reference.fasta \
    --variant input1.vcf \
    --variant input2.vcf \
    --variant input3.vcf \
    --variant input4.vcf \
    --variant input5.vcf \
    --variant input6.vcf \
    -o output.vcf \
    -genotypeMergeOptions UNIQUIFY

Then you can use `VariantsToTable` to turn output.vcf into a table as requested:

    java -jar GenomeAnalysisTK.jar \
    -R reference.fasta -T VariantsToTable \
    -V output.vcf \
    -F CHROM -F POS -F ID -F QUAL -F -GF GT \
    -o output.table