If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Number of mutated reads different between Mutect and IGV

mceredamcereda ItalyMember

Dear All,

I'm sorry for this question but I'm running Mutect on some samples and number of mutated reads ("t_alt_count") are different from the number that I have in IGV.

Here is my call:

java -jar muTect-1.1.4.jar --analysis_type MuTect --enable_extended_output --cosmic ${COSMIC} --dbsnp ${DBSNP138} --input_file:normal ${Nbam} --input_file:tumor ${bam} --out ${id}.out

(no other parameters)

Mutect reports (t_alt_count =6) while in IGV I have 10 mutated reads.

contig position ref_allele alt_allele dbsnp_site covered power tumor_power map_Q0_reads tumor_f t_q20_count t_ref_count t_alt_count
chr21 47537790 C A NOVEL COVERED 0.387407 0.387407 0 0.3 20 14 6 ....

Would it be possible to know which are the default filter on the quality? Do I lose reads for some quality check? How can I set these parameters?



Sign In or Register to comment.