How to call all the allele in samples

Question

[Kritika]

I have snps information for all the samples compared to references. I want all the allele whether snps or match with reference in vcf format How can i achieve this

Sample 1

chr1     26      .       G       A       3046.92  GT:DP:AD:RO:QR:AO:QA:GL 0/1:199:92,107:92:3723:107:4258:-321.956,0,-275.153

Sample 2

chr1     26      .       G       A       3046.92  GT:DP:AD:RO:QR:AO:QA:GL 0/1:199:92,107:92:3723:107:4258:-321.956,0,-275.153

Expected

Sample 1

chr1     1     .      A       A       3046.92  GT:DP:AD:RO:QR:AO:QA:GL 0/0:199:92,107:92:3723:107:4258:-321.956,0,-275.153

Sample 2

chr1     1     .      A       A       3046.92  GT:DP:AD:RO:QR:AO:QA:GL 0/0:199:92,107:92:3723:107:4258:-321.956,0,-275.153

[Pierre Lindenbaum]

how did you get call vcf from the bam ? bcftools ? gatk ?

[Kritika]

Its freebayes i have edited that Actual vcf formats is below

chr1     26      .       G       A       3046.92 .       AB=0.537688;ABP=5.46548;AC=1;AF=0.5;AN=2;AO=107;CIGAR=1X;DP=199;DPB=199;DPRA=0;EPP=3.51765;EPPR=5.3706;GTI=0;LEN=1;MEANALT=1;MQM=58.8598;MQMR=60;NS=1;NUMALT=1;ODDS=596.641;PAIRED=0.383178;PAIREDR=0.586957;PAO=0;PQA=0;PQR=0;PRO=0;QA=4258;QR=3723;RO=92;RPL=19;RPP=99.6307;RPPR=82.4107;RPR=88;RUN=1;SAF=52;SAP=3.19295;SAR=55;SRF=38;SRP=9.05266;SRR=54;TYPE=snp    GT:DP:AD:RO:QR:AO:QA:GL 0/1:199:92,107:92:3723:107:4258:-321.956,0,-275.153

[finswimmer]

Hello Kritika,

could you please describe more precisely what you are trying to do and why. What I see in your example is:

• Setting the REF to the same value as ALT
• Convert the Genotype from het to hom for the new REF
• Change the position of that variant to one

That doesn't make sense to me ...

fin swimmer

[Kritika]

No Usually in VCF file The position will reflect having snps when compared with reference. I want vcf file format where all the positions are called irrelevant of snps / indel or or same allele

[finswimmer]

Ok, than I guess gVCF is what you are looking for.

[Kritika]

What is gvcf. If it will show all positions whatever the nucleotide is called including whether it's homozygous or heterozygous then gvcf will be use full for me

[finswimmer]

Let me google that for you!

First Hit

[WouterDeCoster]

And what is the aim of your analysis, essentially, why do you need all alleles called?

[Kritika]

Is there any way that i keep my sample 1 as reference and call the snps from other samples. Sample 1 i have is bam file.

[Kritika]

My customer wants to know the difference in snps between samples. So if one position the allele is present in one sample which also matching to reference then that allele will not be called out for that sample. But when compared to other samples the allele was reported as snps because it not matching to Reference

[WouterDeCoster]

Gvcf joint calling sounds like the best solution

[Kritika]

Do you know any tool which can help?

[Ram]

gvcf joint calling

DId you try googling that term?

[Kritika]

yes i did google and i uderstood but fro freebayes gvcf option is not working.

[Ram]

Can you please proofread your posts and edit typos? It gets difficult to understand. I think important information such as the tool you're using should be included in your top level post - it is not practical to expect people to read through all your comments to find critical information hidden in them. If you're adding such information in a comment, it would be better to edit your question and add it there as well.

Have you tried looking at GATK? Google doesn't give you just freebayes when you search for "gvcf joint calling", does it? In fact I'm quite certain GATK ranks above freebayes for that particular term. When I search for it (using an incognito tab to avoid biasing the results), the first page is >75% GATK results. Please invest a little more effort.