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Mutect for amplicon based sequencing
Hi, I am running deep targeted sequencing (1000x+) using amplicon based technology on tumour normal pairs and am seeing strange ref and alt allele counts. I am just wondering if Mutect does any sort of internal duplicated reads removal or any other filtering that might be problematic for data with high percentage of duplicates? Specifically I am seeing low alt_count numbers for a lot of variants. For example, for a certain variant visual IGV inspection and GATK HaplotypeCaller give > 30% of alleles being ALT (with over 100 ALT alleles reported), Mutect reports 2 ALT alleles. The same bam file was used in both instances.
Happy to post some vcf data if needed.
Thanks in advance
--analysis_type MuTect --reference_sequence ucsc.hg19.fasta --cosmic CosmicCodingMuts_v68_fixed_sorted.vcf --intervalsregions.bed --input_file:normal.bam --input_file:tumor.bam -vcf f.name.tum.vcf -o f.name.tum,.txt --enable_extended_output --pir_median_threshold 0 --strand_artifact_power_threshold 0
-T HaplotypeCaller -R ucsc.hg19.fasta -I tumor.bam --genotyping_mode DISCOVERY --dbsnp dbsnp_138.hg19.vcf -dcov 1000 -L regions.bed -stand_emit_conf 20 -stand_call_conf 30 -o raw_variants.vcf