I need to index a GTF (gene transfer format) annotation file

Question

[doodle]

I created a GTF file for HLA alleles to be used as a resource for GATK Funcotator. Running Funcotator without indexing the GTF gives this error:

A USER ERROR has occurred: Input funcotator_dataSources.v1.7.20200521s/gencode/hla/hla.annotation.gtf must support random access to enable queries by interval. If it's a file, please index it using the bundled tool IndexFeatureFile

The first few lines of GTF file:

hla_a_01_01_01_01   IMGHLA  gene    1   3503    .   +   .   gene_id "hla_a_01_01_01_01"; gene_name "hla_a_01_01_01_01"; source "IMGHLA";
hla_a_01_01_01_01   IMGHLA  transcript  1   3503    .   +   .   gene_id "hla_a_01_01_01_01"; transcript_id "hla_a_01_01_01_01.1"; gene_name "hla_a_01_01_01_01"; transcript_name "hla_a_01_01_01_01.1";
hla_a_01_01_01_01   IMGHLA  exon    301 373 .   +   .   gene_id "hla_a_01_01_01_01"; transcript_id "hla_a_01_01_01_01.1"; gene_name "hla_a_01_01_01_01"; transcript_name "hla_a_01_01_01_01.1"; exon_number "1"; exon_id "hla_a_01_01_01_01_e_1";
hla_a_01_01_01_01   IMGHLA  exon    504 773 .   +   .   gene_id "hla_a_01_01_01_01"; transcript_id "hla_a_01_01_01_01.1"; gene_name "hla_a_01_01_01_01"; transcript_name "hla_a_01_01_01_01.1"; exon_number "2"; exon_id "hla_a_01_01_01_01_e_2";
hla_a_01_01_01_01   IMGHLA  exon    1015    1290    .   +   .   gene_id "hla_a_01_01_01_01"; transcript_id "hla_a_01_01_01_01.1"; gene_name "hla_a_01_01_01_01"; transcript_name "hla_a_01_01_01_01.1"; exon_number "3"; exon_id "hla_a_01_01_01_01_e_3";

I need to index this file before running Funcotator. I tried using the GATK IndexFeatureFile, as suggested by Funcotator but it gives this error:

A USER ERROR has occurred: Unknown file is malformed: Decoded feature is not valid: hla_a_01_01_01_01   IMGHLA  gene    1   3503    .   +   .   gene_id "hla_a_01_01_01_01"; gene_name "hla_a_01_01_01_01";  source "IMGHLA";
hla_a_01_01_01_01   IMGHLA  transcript  1   3503    .   +   .   gene_id "hla_a_01_01_01_01"; transcript_id "hla_a_01_01_01_01.1"; gene_name "hla_a_01_01_01_01"; transcript_name "hla_a_01_01_01_01.1";
hla_a_01_01_01_01   IMGHLA  exon    301 373 .   +   .   gene_id "hla_a_01_01_01_01"; transcript_id "hla_a_01_01_01_01.1"; gene_name "hla_a_01_01_01_01"; transcript_name "hla_a_01_01_01_01.1"; exon_number 1; exon_id "hla_a_01_01_01_01_e_1";
hla_a_01_01_01_01   IMGHLA  exon    504 773 .   +   .   gene_id "hla_a_01_01_01_01"; transcript_id "hla_a_01_01_01_01.1"; gene_name "hla_a_01_01_01_01"; transcript_name "hla_a_01_01_01_01.1"; exon_number 2; exon_id "hla_a_01_01_01_01_e_2";
hla_a_01_01_01_01   IMGHLA  exon    1015    1290    .   +   .   gene_id "hla_a_01_01_01_01"; transcript_id "hla_a_01_01_01_01.1"; gene_name "hla_a_01_01_01_01"; transcript_name "hla_a_01_01_01_01.1"; exon_number 3; exon_id "hla_a_01_01_01_01_e_3";

Can someone suggest a solution for this or an alternate tool to index the GTF file?

[Pierre Lindenbaum]

cross posted: https://stackoverflow.com/questions/78996218/

Answer 1

[Pierre Lindenbaum]

The error is here: https://github.com/broadinstitute/gatk/blob/2ba3a15d9f49a675f38641e652418667aabc6161/src/main/java/org/broadinstitute/hellbender/utils/codecs/gtf/AbstractGtfCodec.java#L235

GATK fails if the GTF doesn't contain the gene_type : https://github.com/broadinstitute/gatk/blob/2ba3a15d9f49a675f38641e652418667aabc6161/src/main/java/org/broadinstitute/hellbender/utils/codecs/gtf/AbstractGtfCodec.java#L401