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?

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