S2 Table. Different parameters for variant calling in Ion Torrent Variant
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S2 Table. Different parameters for variant calling in Ion Torrent Variant
Different parameters for variant calling in Ion Torrent Variant Caller for Ion PGM and Ion PGM Dx. Parameter. (Torrent Variant Caller Settings). Ion. PGM. Ion.
S2 Table. Different parameters for variant calling in Ion Torrent Variant Caller for Ion PGM and Ion PGM Dx Parameter Ion Ion Recommended (Torrent Variant Caller Settings) PGM PGM values Dx snp_min_allele_freq snp_Minimum allele 0.15 0.1 0.01-0.2 frequency snp_min_variant_score snp_Minimum 10 10 ≥ 10 quality snp_strand_bias snp_Maximum strand 0.9 0.95 1 bias hotspot_min_allele_freq hotspot_Minimum 0.15 0.1 NA allele frequency hotspot_min_variant_score hotspot_Minimum 10 10 ≥ 10 quality hotspot_strand_bias hotspot_Maximum 0.9 0.95 1 strand bias indel_min_allele_freq indel_min_allele_freq 0.15 0.1 0.05-0.2 indel_min_variant_score indel_strand_bias heavy_tailed outlier_probability
do_snp_realignment
prediction_precision
downsample_to_coverage
suppress_recalibration
indel_Minimum quality indel_Maximum strand bias T-distribution tails prior probability that a read comes from some other distribution realign reads in the vicinity of SNP candidates number of pseudodata-points suggesting our predictions match the measurements without bias reduce coverage in over-sampled locations to this value ignore the base recalibration
10
10
≥ 10
0.9
0.95
1
3
default
NA
0.01
default
0.005-0.01
0
0
0: germline
1
default
1
400
400
400: germline
1
default
1: ignore base calibration
values from pipeline in TVC FreeBayes module setting allow_indels allow_mnps allow_SNPS gen_min_alt_allele_freq
Enable indels Enable MNPs Enable SNPs Early-on filter for allele frequency gen_min_coverage Early-on filter for minimum coverage gen_min_indel_alt_allele_freq An early-on filter for allele frequency for indel callings min_base_qv min_mapping_qv Minimum mapping quality read_max_mismatch_fraction Maximum fraction of mismatches allowed in the length of read read_mismatch_limit Number of mismatches allowed
