Test-drive the GATK tools and Best Practices pipelines on Terra
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Why do I get Reject when it should be Keep
Hello, Would you please let us know why below sample field has been rejected rather than keep:
contig position ref_allele alt_allele score dbsnp_site covered power tumor_power normal_power total_pairs improper_pairs map_Q0_reads t_lod_fstar tumor_f contaminant_fraction contaminant_lod t_ref_count t_alt_count t_ref_sum t_alt_sum t_ins_count t_del_count normal_best_gt init_n_lod n_ref_count n_alt_count n_ref_sum n_alt_sum judgement chr5 112164616 C T 0 NOVEL COVERED 1 1 1 1905 168 0 670.750479 0.294294 0.02 32.630413 470 196 18315 7525 6 0 CC 218.268391 738 1 28645 37 REJECT
We appreciate all your help. Thank you