How to convert a raw vcf to a phased vcf

Question

[pinn]

Hi,

I generated a vcf file called variants using Freebayes. Further, I would like to perform normalisation for my vcf file I found a tool BAN does the job. But it asking a phased vcf file as input how to get a phased file any tools. I'm not able to understand what is the difference between unphased and phased ? Is their any other tools for normalisation of vcf ?

thanks for your comments

Answer 1

[Pierre Lindenbaum]

I'm not able to understand what is the difference between unphased and phased ?

variant1: 0/1 variant2: 0/1

are unphased we're not sure if variant 1 and 2 belong to the same homologous chromosome.

variant1: 0|1 variant2: 0|1

are phased they are on the same homologous chromosome.

how to get a phased file any tools.

try gatk ReadBackedPhasing https://software.broadinstitute.org/gatk/documentation/article?id=45

(the main page has moved for ReadBackedPhasing , I cannot find it...)

[pinn]

I converted to phased format using other tool Beagle 4.1.

some of the Chr showing random what it exactly mean ?

**Phased VCF**
chr14_GL000009v2_random    872    .    G    T    .    PASS    .    GT    1|1
chr14_GL000009v2_random    3773    .    T    C    .    PASS    .    GT    1|1
chr14_GL000009v2_random    19142    .    C    A    .    PASS    .    GT    1|1
chr14_GL000009v2_random    19161    .    T    C    .    PASS    .    GT    1|1
chr14_GL000009v2_random    19191    .    C    A    .    PASS    .    GT    1|1
chr14_GL000009v2_random    19228    .    A    G    .    PASS    .    GT    1|1
chr14_GL000009v2_random    19295    .    G    T    .    PASS    .    GT    1|1
chr14_GL000009v2_random    35748    .    G    A    .    PASS    .    GT    1|1
chr14_GL000009v2_random    36037    .    C    T    .    PASS    .    GT    0|1
chr14_GL000009v2_random    36293    .    C    T    .    PASS    .    GT    0|1
chr14_GL000009v2_random    40265    .    C    T    .    PASS    .    GT    0|1
chr14_GL000009v2_random    42944    .    T    A    .    PASS    .    GT    1|0
chr14_GL000009v2_random    42954    .    T    C    .    PASS    .    GT    0|1
chr14_GL000009v2_random    42982    .    T    G    .    PASS    .    GT    0|1
chr14_GL000009v2_random    46937    .    T    C    .    PASS    .    GT    1|0
chr14_GL000009v2_random    47670    .    T    C    .    PASS    .    GT    0|1
chr14_GL000009v2_random    47869    .    T    C    .    PASS    .    GT    1|0
chr14_GL000009v2_random    47883    .    T    C    .    PASS    .    GT    1|1
chr14_GL000009v2_random    48147    .    A    G    .    PASS    .    GT    1|1
chr14_GL000009v2_random    48854    .    G    A    .    PASS    .    GT    0|1

[Pierre Lindenbaum]

Additional Data In Human Genome (Hg18 / Hg19) Assembly ?

[pinn]

Hi Even though I mapped my bam with a latest ref.fa (hg38) how come I'm getting additional data from hg18/hg19 assembly. What would be the reason. Whether this additional information can result in FP and FN (false positives and false negatives) variants ?