Failure to annotate variants with dbNSFP

[mzekavat]

I'm running the following script:

/psych/genetics_data/working/cseed/bin/hail read -i ${input_vds} \ annotatevariants tsv file:///medpop/esp2/mzekavat/Estonia/UPDATED_TOOLS/dbNSFPv3.2/dbNSFP3.2a.ALLChr.bgz \ -r va.dbNSFP \ -t 'SIFT_pred: String, PROVEAN_pred: String, Polyphen2_HDIV_pred: String, Polyphen2_HVAR_pred: String, LRT_pred: String, MutationTaster_pred: String, MutationAssessor_pred: String, FATHMM_pred: String, MetaSVM_pred: String, MetaLR_pred: String, CADD_phred: Double, Eigen-raw: Double, Eigen-phred: Double, Eigen-raw_rankscore: Double' \ -v "#chr,pos(1-based),ref,alt" \ -m "." \ annotatevariants expr -c 'va.of8 = (if ("D" ~ va.dbNSFP.SIFT_pred) 1 else 0) + (if ("D" ~ va.dbNSFP.PROVEAN_pred) 1 else 0) + (if ("D" ~ va.dbNSFP.Polyphen2_HDIV_pred) 1 else 0) + (if ("D" ~ va.dbNSFP.Polyphen2_HVAR_pred) 1 else 0) + (if ("D" ~ va.dbNSFP.LRT_pred) 1 else 0) + (if ("H" ~ va.dbNSFP.MutationAssessor_pred || "M" ~ va.dbNSFP.MutationAssessor_pred) 1 else 0) + (if ("D" ~ va.dbNSFP.MutationTaster_pred) 1 else 0) + (if ("D" ~ va.dbNSFP.FATHMM_pred) 1 else 0)' \ exportvariants -c 'v.contig,v.start,v.ref,v.alt,va.of8,va.dbNSFP.MetaSVM_pred,va.dbNSFP.MetaLR_pred,va.dbNSFP.CADD_phred,va.dbNSFP.Eigen-raw,va.dbNSFP.Eigen-phred,va.dbNSFP.Eigen-raw_rankscore' -o /user/mzekavat/MiGen/dbNSFP.MiGen.tsv

and I'm getting an error here: /medpop/esp2/mzekavat/MiGen/Annotation/hail.log Would greatly appreciate thoughts on this as soon as possible!

[tpoterba]

Maryam, I ran this command in Unix:

gunzip -c  <file> | cut -f4 | sort | uniq -c
20709505 A
20934670 C
20968049 G
20693812 T
     25 alt

I think the problem is that the headers from all the files were included in the one file. I'm running another grep now to be sure.

I'll fix the error message though!

[tpoterba]

Problem was variants in the dbnsfp file with ref == alt