The best solution for one-to-one correspondence between genes and transcripts

[user-tq]

The best solution for one-to-one correspondence between genes and transcripts

[user-tq]

In order to obtain as many transcripts as possible corresponding to genes,i do

zcat   /mnt/tool/software_tq/myscript/MANE.GRCh38.v1.0.summary.txt.gz |awk -F'\t' '{print $4,$6,$8,$10}'|grep 'MANE Select'|awk '{print $3}'|awk -F. '{print $1}'  > MANE.list

vcf2maf.pl --input-vcf ../vcfs/patient101.vcf --output-maf    test_patient101.maf             --tumor-id patient101.tumor             --ref-fasta /mnt/tool/ref_source/iGenomes/references/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta             --vep-data /mnt/script/tanq/snakemake/ngs-pipeline/vep_cache             --ncbi-build GRCh37             --vep-path $vep_path             --maf-center mane_test             --normal-id patient101.normal  --vep-overwrite   --verbose    --custom-enst  MANE.list ```

In the end, I realized that this was a bad idea, based on the KMT2B I annotated
in vep grch37
KMT2B-ENST00000222270-NM_014727.1

KMT2B,frameshift_variant,p.Asp375GlufsTer11,ENST00000222270,NM_014727.1;
KMT2B,frameshift_variant,p.Asp375GlufsTer11,ENST00000420124,;
KMT2B,frameshift_variant,p.Asp375GlufsTer11,ENST00000341701,;
ZBTB32,downstream_gene_variant,,ENST00000262630,NM_014383.1;
ZBTB32,downstream_gene_variant,,ENST00000392197,;
ZBTB32,downstream_gene_variant,,ENST00000426659,;
KMT2B,non_coding_transcript_exon_variant,,ENST00000607650,;
KMT2B,non_coding_transcript_exon_variant,,ENST00000606995,;
ZBTB32,downstream_gene_variant,,ENST00000481182,;

but in MANE select (base on GRCh38)
KMT2B-NM_014727.3-ENST00000420124.4