ERROR running annovar with cosmic90
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2.2 years ago
Laven9 • 0

I am trying to run annovar with cosmic90. When preparing files, I follow the command:

prepare_annovar_user.pl -dbtype cosmic .CosmicMutantExport.tsv -vcf CosmicCodingMuts.vcf > hg38_cosmic90_coding.txt

But it went wrong, with error:COSMIC MutantExport format error: column 17 or 12 should be 'Mutation ID' or 'ID_NCV'

Then I use

sed -i 's/\<MUTATION_ID\>/Mutation ID/g'

to tranfer.

But it still went wrong with the same error.

So I check the 'Mutaion ID''s position, and found:

 [1] "1"                        "Gene name"                "Accession Number"         "Gene CDS length"         
 [5] "HGNC ID"                  "Sample name"              "ID_sample"                "ID_tumour"               
 [9] "Primary site"             "Site subtype 1"           "Site subtype 2"           "Site subtype 3"          
[13] "Primary histology"        "Histology subtype 1"      "Histology subtype 2"      "Histology subtype 3"     
[17] "Genome-wide screen"       "GENOMIC_MUTATION_ID"      "LEGACY_MUTATION_ID"       "Mutation ID"             
[21] "Mutation CDS"             "Mutation AA"              "Mutation Description"     "Mutation zygosity"       
[25] "LOH"                      "GRCh"                     "Mutation genome position" "Mutation strand"         
[29] "SNP"                      "Resistance Mutation"      "FATHMM prediction"        "FATHMM score"            
[33] "Mutation somatic status"  "Pubmed_PMID"              "ID_STUDY"                 "Sample Type"             
[37] "Tumour origin"            "Age"

it is the NO.20

I think I might exchange it with column 17, but I am not sure if it will make annovar went wrong and got bad result.

Please give me some advice! Thank you!

annovar cosmic • 1.3k views
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Please use 101010 button to format any commands/code for better readability.

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2.1 years ago
s.awasthy ▴ 10

From the description of file CosmicMutantExport.tsv column 17 is GENOMIC_MUTATION_ID so use it in a way:

sed -i 's/\<\GENOMIC_MUTATION_ID>/Mutation ID/g'

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It should be: sed 's/GENOMIC_MUTATION_ID/Mutation ID/' (without < or >)

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