Did anyone success in working with the broad ABSOLUTE?
Entering edit mode
7.2 years ago
bioinflix ▴ 70

Recently I have tried the broad ABSOLUTE package several times with my exome-seq data and noticed that it can also be run under the GenePattern public server. I feed it with my copy-number segmented file together with the somatic point muation MAF file, but only got the error report:

"Error: min.mut.af is required if a file is provided for maf.fn" 

since I set the min.mut.af value when using the maf.fn file. I also tried to run it under R following the documentation and still it can't work.

The segmented file format:

"Chromosome", "Start", "End", "Num_Probes" and "Segment_Mean" 

And the MAF file format:

Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID HGVSc HGVSp HGVSp_Short Transcript_ID Exon_Number t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count all_effects Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation ALLELE_NUM DISTANCE STRAND SYMBOL SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL CCDS ENSP SWISSPROT TREMBL UNIPARC RefSeq SIFT PolyPhen EXON INTRON DOMAINS GMAF AFR_MAF AMR_MAF ASN_MAF EUR_MAF AA_MAF EA_MAF CLIN_SIG SOMATIC PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE

The file format should be as the same as what ABSOLUTE required, not very clear how exactly the package can be work. 

ABSOLUTE MAF • 2.7k views
Entering edit mode

Hello bioinflix !

It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?p=153628

This is typically not recommended as it runs the risk of annoying people in both communities.

Entering edit mode

Please ignore that and it seems that post can not been deleted. Maybe this forum can be much proper, although I hope I could get more answers for this confusion.

Entering edit mode
6.6 years ago
shlee ▴ 60

The min.mut.af (minimum mutation allelic fraction) failure was a bug that has now been fixed for GenePattern's ABSOLUTE, which is still in beta. The algorithm is the same (v1.0.6) and the updated GenePattern module version is v1.4. 



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