Call "KEEP" "REJECT" option to fine tune filters for poor_mapping_region_alternate_allele_mapq fail
I am using the the MuTech program in standard conditions (with --enable_extended_output) with a matched Normal/tumor couple with the
following code at TP53 locus. We have confirmed the presence of a mutation in this tumor by sanger sequencing at chr17 position 7578526.
I used the following code :
java -Xmx2g -jar muTect-1.1.1.jar --analysis_type MuTect --reference_sequence fusion2.fasta --enable_extended_output --dbsnp dbsnp_132_b37.leftAligned.vcf --cosmic b37_cosmic_v54_120711.vcf --intervals chr17:7571720-7590868 --input_file:normal bloodsorted.sorted.bam --input_file:tumor Tumor02878.sorted.bam --out result.call_stats.txt --coverage_file example.coverage.wig.txt
Using MuTech, mutation at this position get the judgement 'REJECT'. I looked in the extended output and found the the reason of failure
was : poor_mapping_region_alternate_allele_mapq.
I am puzzle, any suggestions ? (I attach file result result.call_stats.txt)
I would like to decrease the stringency of the coresponding filter to get the judgement 'KEEP' for the mutation that was confirmed. I was unable to find which option to use in the program and with which value ( I tried --required_maximum_alt_allele_mapping_quality_score option with different values but it did not change 'KEEP", "REJECT" status).
Hope I was clear in my explanations, I am new in the forum and not used to post question.