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lgmgeo / AnnotSV

Annotation and Ranking of Structural Variation
GNU General Public License v3.0
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'TAD_coordinate' and 'ENCODE_experiment' columns missing in 3.4.2 result #253

Closed Stikus closed 2 months ago

Stikus commented 2 months ago

Hello, after update from 3.3.6 to 3.4.2 our output lost TAD_coordinate and ENCODE_experiment columns.

I haven't found any info about it in changelog - that's why I'm asking is this intended.

Command: '/soft/AnnotSV-3.4.2/bin/AnnotSV -annotationsDir /ref/AnnotSV/3.4.2 -genomeBuild GRCh37 -SVinputFile /inputs/som_diploidSV.vcf -outputFile /outputs/test_som.annotsv.tsv '.

AnnotSV_ID;SV_chrom;SV_start;SV_end;SV_length;SV_type;Samples_ID;ID;REF;ALT;QUAL;FILTER;INFO;FORMAT;chr19;Annotation_mode;CytoBand;Gene_name;Closest_left;Closest_right;Gene_count;Tx;Tx_version;Tx_start;Tx_end;Overlapped_tx_length;Overlapped_CDS_length;Overlapped_CDS_percent;Frameshift;Exon_count;Location;Location2;Dist_nearest_SS;Nearest_SS_type;Intersect_start;Intersect_end;RE_gene;P_gain_phen;P_gain_hpo;P_gain_source;P_gain_coord;P_loss_phen;P_loss_hpo;P_loss_source;P_loss_coord;P_ins_phen;P_ins_hpo;P_ins_source;P_ins_coord;po_P_gain_phen;po_P_gain_hpo;po_P_gain_source;po_P_gain_coord;po_P_gain_percent;po_P_loss_phen;po_P_loss_hpo;po_P_loss_source;po_P_loss_coord;po_P_loss_percent;P_snvindel_nb;P_snvindel_phen;B_gain_source;B_gain_coord;B_gain_AFmax;B_loss_source;B_loss_coord;B_loss_AFmax;B_ins_source;B_ins_coord;B_ins_AFmax;B_inv_source;B_inv_coord;B_inv_AFmax;po_B_gain_allG_source;po_B_gain_allG_coord;po_B_gain_someG_source;po_B_gain_someG_coord;po_B_loss_allG_source;po_B_loss_allG_coord;po_B_loss_someG_source;po_B_loss_someG_coord;GC_content_left;GC_content_right;Repeat_coord_left;Repeat_type_left;Repeat_coord_right;Repeat_type_right;Gap_left;Gap_right;SegDup_left;SegDup_right;ENCODE_blacklist_left;ENCODE_blacklist_characteristics_left;ENCODE_blacklist_right;ENCODE_blacklist_characteristics_right;ACMG;HI;TS;DDD_HI_percent;ExAC_delZ;ExAC_dupZ;ExAC_cnvZ;ExAC_synZ;ExAC_misZ;GenCC_disease;GenCC_moi;GenCC_classification;GenCC_pmid;NCBI_gene_ID;OMIM_ID;OMIM_phenotype;OMIM_inheritance;OMIM_morbid;OMIM_morbid_candidate;LOEUF_bin;GnomAD_pLI;ExAC_pLI;AnnotSV_ranking_score;AnnotSV_ranking_criteria;ACMG_class

Command: '/soft/AnnotSV-3.3.6/bin/AnnotSV -annotationsDir /ref/AnnotSV/3.3.6 -genomeBuild GRCh37 -SVinputFile /inputs/som_diploidSV.vcf -outputFile /outputs/test_som.annotsv.tsv '.

AnnotSV_ID;SV_chrom;SV_start;SV_end;SV_length;SV_type;Samples_ID;ID;REF;ALT;QUAL;FILTER;INFO;FORMAT;chr19;Annotation_mode;CytoBand;Gene_name;Gene_count;Tx;Tx_start;Tx_end;Overlapped_tx_length;Overlapped_CDS_length;Overlapped_CDS_percent;Frameshift;Exon_count;Location;Location2;Dist_nearest_SS;Nearest_SS_type;Intersect_start;Intersect_end;RE_gene;P_gain_phen;P_gain_hpo;P_gain_source;P_gain_coord;P_loss_phen;P_loss_hpo;P_loss_source;P_loss_coord;P_ins_phen;P_ins_hpo;P_ins_source;P_ins_coord;po_P_gain_phen;po_P_gain_hpo;po_P_gain_source;po_P_gain_coord;po_P_gain_percent;po_P_loss_phen;po_P_loss_hpo;po_P_loss_source;po_P_loss_coord;po_P_loss_percent;P_snvindel_nb;P_snvindel_phen;B_gain_source;B_gain_coord;B_gain_AFmax;B_loss_source;B_loss_coord;B_loss_AFmax;B_ins_source;B_ins_coord;B_ins_AFmax;B_inv_source;B_inv_coord;B_inv_AFmax;po_B_gain_allG_source;po_B_gain_allG_coord;po_B_gain_someG_source;po_B_gain_someG_coord;po_B_loss_allG_source;po_B_loss_allG_coord;po_B_loss_someG_source;po_B_loss_someG_coord;TAD_coordinate;ENCODE_experiment;GC_content_left;GC_content_right;Repeat_coord_left;Repeat_type_left;Repeat_coord_right;Repeat_type_right;Gap_left;Gap_right;SegDup_left;SegDup_right;ENCODE_blacklist_left;ENCODE_blacklist_characteristics_left;ENCODE_blacklist_right;ENCODE_blacklist_characteristics_right;ACMG;HI;TS;DDD_HI_percent;ExAC_delZ;ExAC_dupZ;ExAC_cnvZ;ExAC_synZ;ExAC_misZ;GenCC_disease;GenCC_moi;GenCC_classification;GenCC_pmid;OMIM_ID;OMIM_phenotype;OMIM_inheritance;OMIM_morbid;OMIM_morbid_candidate;LOEUF_bin;GnomAD_pLI;ExAC_pLI;AnnotSV_ranking_score;AnnotSV_ranking_criteria;ACMG_class

Maybe it is result of Exomiser annotation 2202 -> 2402 update.

lgmgeo commented 2 months ago

You are right, nothing in the changelog. There has been no new modification in the AnnotSV code. The information is located in the README: image

Actually, TAD annotations are no longer distributed by AnnotSV because each user needs different ENCODE experiments (with its good “Analysis” / ”Genome assembly”).

You need to download the ENCODE data of interest for your own usage. You can have more information on how to do in the README, section "TAD boundaries annotations".

However, an easy thing to do if you are satisfied with the TAD v3.3.6 annotations is to copy the files from the v3.3.6 install into the v3.4.2 install: “$ANNOTSV/share/AnnotSV/Annotations_Human/FtIncludedInSV/TAD/GRCh37” and/or “$ANNOTSV/share/AnnotSV/Annotations_Human/ FtIncludedInSV/TAD/GRCh38” directories.

Maybe it is result of Exomiser annotation 2202 -> 2402 update.

No link.

Best, Véronique

Stikus commented 2 months ago

Thank you for fast answer, missed this part of README. We'll look into it.