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.

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



Sign In or Register to comment.