Comments (3)
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
from vcf2maf.
Related Issues (20)
- --ref-fasta is not the same genome build as your --input-vcf. at vcf2maf.pl line 410 HOT 2
- Losing info when reading maf file
- Empty 't_depth' 't_ref_count' 't_alt_count' HOT 1
- Add options for RefSeq and Merged caches when converting to MAF
- ERROR: Failed to run the VEP annotator! HOT 2
- Running error HOT 3
- Why is empty in all database? HOT 1
- Option --retain-fmt doesn't work
- ERROR: Provided --ref-fasta is missing or empty HOT 3
- Update vcf2maf to work with later Ensembl vep releases HOT 2
- Release new tag HOT 4
- ensg_to_entrez_id_map_ensembl_feb2014.tsv erroneously assigns Entrez ID
- ERROR: Failed to run the VEP annotator!
- VCF2MAF and allele frequency HOT 4
- cosmic annotation
- HGVSc + HGVSp + HGVSp_Short not available after vcf2maf from an annotated VCF from sarek with VEP v108 HOT 3
- Error Argument "" isn't numeric in subtraction HOT 2
- WARNING: Unrecognized effect "sequence_feature". Assigning lowest priority! HOT 1
- Unrecognized biotype/effect HOT 2
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from vcf2maf.