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Number of mutated reads different between Mutect and IGV

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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