A: comparing vcf files of disease (affected) and normal (unaffected) samples

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8.6 years ago

ramanandan.prabhakaran ▴ 20

Dear friends,

My requirement is to find list of variants which are present in affected but not in unaffected samples, then I have to prepare a list For example,

Samples           4:1243-SNV     5:1277-SNV       15:4070-SNV    ….. ….. …… …… ….. …..      16:5335-SNV 
A(affected)       C_T            A_G              A_T            ….. ….. …… …… ….. …..      A_C
B(unaffected)     C_C            A_A              A_A            ….. ….. …… …… ….. …..      A_A
C(affected)       C_T            A_G              A_T            ….. ….. …… …… ….. …..      A_C
D(affected)       C_T            A_G              A_T           ….. ….. …… …… ….. …..       A_C

Any help friends.

I generated the vcf files using GATK tool.

Variant-calling VCF genotype SNP • 2.3k views

ADD COMMENT • link updated 2.4 years ago by Ram 43k • written 8.6 years ago by ramanandan.prabhakaran ▴ 20

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vcftools will be helpful in this case.

ADD REPLY • link updated 2.4 years ago by Ram 43k • written 8.6 years ago by Ashutosh Pandey 12k

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Thanks Ashutosh for your suggestion.

ADD REPLY • link updated 2.4 years ago by Ram 43k • written 8.6 years ago by ramanandan.prabhakaran ▴ 20

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