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.
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