Dragen

ATAV program launch file

From (old command):

/nfs/goldstein/software/sh/atav.sh

To (new command):

/nfs/goldstein/software/sh/atav_dragen.sh

Important note:
  1. atav_dragen.sh will automatically execute qsub command to allocate proper compute resources. Please DO NOT qsub your ATAV job; just run it directly on the submit host.
  2. Not all your AnnoDB samples are in new DragenDB, ATAV Dragen will output a new sample file when detected problem samples and output to your --out dir named "existing.sample.txt".

Command option changes:

  • --function --> --effect

New effect input format: impact:effect , Ex. HIGH:start_lost
New effect reference files located: /nfs/goldstein/software/atav_home/data/effect
Order of effects from most damaging to least damaging:

+----+----------+---------------------------------------------------+
| id | impact   | effect                                            |
+----+----------+---------------------------------------------------+
|  1 | HIGH     | chromosome_number_variation                       |
|  2 | HIGH     | exon_loss_variant                                 |
|  3 | HIGH     | frameshift_variant                                |
|  4 | HIGH     | rare_amino_acid_variant                           |
|  5 | HIGH     | splice_acceptor_variant                           |
|  6 | HIGH     | splice_donor_variant                              |
|  7 | HIGH     | start_lost                                        |
|  8 | HIGH     | stop_gained                                       |
|  9 | HIGH     | stop_lost                                         |
| 10 | HIGH     | transcript_ablation                               |
| 11 | HIGH     | gene_fusion                                       |
| 12 | HIGH     | bidirectional_gene_fusion                         |
| 13 | MODERATE | 3_prime_UTR_truncation+exon_loss_variant          |
| 14 | MODERATE | 5_prime_UTR_truncation+exon_loss_variant          |
| 15 | MODERATE | coding_sequence_variant                           |
| 16 | MODERATE | disruptive_inframe_deletion                       |
| 17 | MODERATE | disruptive_inframe_insertion                      |
| 18 | MODERATE | conservative_inframe_deletion                     |
| 19 | MODERATE | conservative_inframe_insertion                    |
| 20 | MODERATE | missense_variant+splice_region_variant            |
| 21 | MODERATE | missense_variant                                  |
| 22 | MODERATE | regulatory_region_ablation                        |
| 23 | MODERATE | splice_region_variant                             |
| 24 | MODERATE | TFBS_ablation                                     |
| 25 | LOW      | 5_prime_UTR_premature_start_codon_gain_variant    |
| 26 | LOW      | initiator_codon_variant                           |
| 27 | LOW      | initiator_codon_variant+non_canonical_start_codon |
| 28 | LOW      | splice_region_variant+synonymous_variant          |
| 29 | LOW      | splice_region_variant                             |
| 30 | LOW      | start_retained                                    |
| 31 | LOW      | stop_retained_variant                             |
| 32 | LOW      | synonymous_variant                                |
| 33 | MODIFIER | 3_prime_UTR_variant                               |
| 34 | MODIFIER | 5_prime_UTR_variant                               |
| 35 | MODIFIER | coding_sequence_variant                           |
| 36 | MODIFIER | conserved_intergenic_variant                      |
| 37 | MODIFIER | conserved_intron_variant                          |
| 38 | MODIFIER | downstream_gene_variant                           |
| 39 | MODIFIER | exon_variant                                      |
| 40 | MODIFIER | feature_elongation                                |
| 41 | MODIFIER | feature_truncation                                |
| 42 | MODIFIER | gene_variant                                      |
| 43 | MODIFIER | intergenic_region                                 |
| 44 | MODIFIER | intragenic_variant                                |
| 45 | MODIFIER | intron_variant                                    |
| 46 | MODIFIER | mature_miRNA_variant                              |
| 47 | MODIFIER | miRNA                                             |
| 48 | MODIFIER | NMD_transcript_variant                            |
| 49 | MODIFIER | non_coding_transcript_exon_variant                |
| 50 | MODIFIER | non_coding_transcript_variant                     |
| 51 | MODIFIER | regulatory_region_amplification                   |
| 52 | MODIFIER | regulatory_region_variant                         |
| 53 | MODIFIER | TF_binding_site_variant                           |
| 54 | MODIFIER | TFBS_amplification                                |
| 55 | MODIFIER | transcript_amplification                          |
| 56 | MODIFIER | transcript_variant                                |
| 57 | MODIFIER | upstream_gene_variant                             |
+----+----------+---------------------------------------------------+
  • --ctrl-maf --> --ctrl-af
  • --loo-maf --> --loo-af
  • --exac-maf --> --exac-af
  • --var-status --> --filter

new cutoff input values: PASS, LIKELY, INTERMEDIATE, FAIL (using comma delimited)
old cutoff input values: PASS, INTERMEDIATE, FAIL

  • --min-coverage

new cutoff input values: 10, 20, 30, 50, 200
old cutoff input values: 3, 10, 20, 200

  • --hap-score no longer support

New filters:

  • --sor: specify a maximum strand Odds ratio.

--snv-sor: specify a minimum strand Odds ratio for SNVs.
--indel-sor: specify a minimum strand Odds ratio for indels.

Output field changes:

  • Function --> Effect
  • Gene Transcript (AA Change) --> All Effect Gene Transcript HGVS_p
  • Genotype --> GT
  • Gatk Filtered Coverage --> DP
  • DP Bin
  • Pass Fail Status --> FILTER
  • Case MAF --> Case AF
  • Ctrl MAF --> Ctrl AF
  • LOO MAF --> LOO AF
  • ExAC {pop} maf --> ExAC {pop} af
  • Is Minor Ref no longer support
  • Vqslod no longer support
  • Haplotype Score no longer support

Other changes:

  • CCDS reference file

From (old file):

/nfs/goldstein/software/atav_home/data/ccds/addjusted.CCDS.genes.index.r14.txt

To (new file):

/nfs/goldstein/software/atav_home/data/ccds/addjusted.CCDS.genes.index.r20.hg19.txt