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TransVar - multiway annotator for precision medicine

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panno batch example

XimenaBo opened this issue · comments

commented

Hello,

This is so far a great tool, thanks!
I cannot, however, process proteinvariants in batches.
it works well with a single event:

transvar panno -i 'PIK3CA:p.H1047R' --refseq

input transcript gene strand coordinates(gDNA/cDNA/protein) region info PIK3CA:p.H1047R NM_006218.2 (protein_coding) PIK3CA + chr3:g.178952085A>G/c.3140A>G/p.H1047R inside_[cds_in_exon_21] CSQN=Missense;reference_codon=CAT;candidate_codons=AGG,AGA,CGA,CGC,CGG,CGT;candidate_mnv_variants=chr3:g.178952085_178952086delATinsGA,chr3:g.178952085_178952086delATinsGC,chr3:g.178952085_178952086delATinsGG,chr3:g.178952084_178952086delCATinsAGG,chr3:g.178952084_178952086delCATinsAGA;dbxref=GeneID:5290,HGNC:8975,MIM:171834;aliases=NP_006209;source=RefSeq

But if I give it a file as input (one protein HGVS per row), the return is empty (just the header:
transvar panno -i test_variants.txt --refseq
input transcript gene strand coordinates(gDNA/cDNA/protein) region info

How should i submit panno batches? Is this possible as ganno is? I really hope so crosses fingers
Thanks a lot in advance!

commented

Hi @XimenaBo ,

Correct option to pass a file listing variants to panno is -l (see transvar panno --help)

  -i I                  <gene/chrm>:<mutation>, E.g., MET:1010, PIK3CA:E545K,
                        PIK3CA:c.1633G>A, chr12:25398285
  -l L                  mutation list file

Hope this helps !
Have a nice day,
Felix.