MuTect2 VCF file

Question

[a.james]

Hello All,

Can anyone help me with interpreting VCF file file from Mutect2 variant calling.. I have followed the methods described for calling variants. The samples I am using are Tumor-Normal matching samples.

The resulting VCF file looks different from regular VCF file. I couldn't find any information regarding for interpreting the VCf file from MuTect2 caller.

Here is an example variant from the VCF file called using MuTect2

chrY 10036237 . A C . alt_allele_in_normal ECNT=1;HCNT=11;MAX_ED=.;MIN_ED=.;NLOD=8.64;TLOD=7.11 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/0:86,8:0.091:7:1:0.125:2491,167:60:26

Where in all of the variants reported from my samples I have only alt_allele_in_normal information no information from tumor sample.Any help would be great

Thank you

[joyce.lefay]

Hi, I have the same problem. Did you find the way to solve it? Thank you

[vincent]

Hi, I also encountered this problem; after some testing, I found that the sample name in your .bam files is the point.

You can extract sample name from bam file by this command :

samtools view -H test.bam | grep '^@RG' | sed "s/.*SM:\([^\t]*\).*/\1/g" | uniq

However, If the sample names in your tumor and normal bam files are the same, i.e. tumor1 in your case, the vcf file only has one tumor1 column. So you should change your sample names in your bam files by this command:

samtools view -H test.bam  | sed "s/SM:[^\t]*/SM:TEST_SAMPLE_NAME/g" | samtools reheader - test.bam > test_SM.bam

Hope it helps.

Answer 1

[igor]

There is an explanation on the GATK discussion board

[izzy.yichao.cai]

Hi I think the link is dead and I am also struggling with getting the full documentation of the fields reported in Mutect2 VCF file.

Answer 2

[EagleEye]

http://www.broadinstitute.org/cancer/cga/mutect_run