This question was also asked on Biostars
I have multiple vcf of CASES and CONTROLS variations annotated by VEP, SNPEff and SnpSift.
- First pair vcf -> only variations| CASES and CONTROLS
- Second pair vcf -> variations + SnpEff | CASES and CONTROLS
- Third pair vcf-> variations + SnpEff+VEP+SnpSIFT| CASES and CONTROLS | at so on The data has non-overlapping samples. I tried to merge corresponding vcf of CASE and CONTROLS into one file with bcftools merge.
The code is:
bgzip -c file.vcf > file.vcf.gz
tabix -p vcf file.vcf.gz
bcftools merge -o merged.vcf.gz -Oz file.vcf.gz file_2.vcf.gz
Unfortunatelly in files with SnpSift annotations i got this error:
Error at chr1:20724637: wrong number of fields in dbNSFP_ada_score?
Please anybody knows how to solved this error or what does it mean?
grep header:
INFO=<ID=dbNSFP_ada_score,Number=A,Type=String,Description="Field 'ada_score' from dbNSFP">
-G on chr1:
CHROM POS ID REF ALT QUAL FILTER INFO
chr1 20724637 rs1280663306;rs1445195248 TGGGAGGGAGGGAGAGAGGT TGGGAGGGAGAGAGGT,TGGGAGGGAGGGAGGGAGGT,TGGGAGGGAGGGAGAGAGGG,TGGGGGGGAGGGAGAGAGGT,TGGGTGGGAGGGAGAGAGGT,TGGGAGAGAGGGAGAGAGGT 2.42927 . ANN=TGGGGGGGAGGGAGAGAGGT|splice_region_variant&intron_variant|LOW|SH2D5|SH2D5...SNV|1||||||||||||||||||||||||||||||||||||||||||||;dbNSFP_ada_score=1.43020658327008E-4,0.00157457299236331,5.16496450143413E-5;dbNSFP_rf_score=0.016,0.054,0.0;dbNSFP_PHRED=5.632,0.077,6.365,7.459,2.716
chr1 20724637 rs1280663306;rs1445195248 TGGGAGGGAGGGAGAGAGGT TGGGAGGGAGAGAGGT,TGGGAGGGAGGGAGGGAGGT,TGGGAGGGAGGGAGAGAGGG,TGGGGGGGAGGGAGAGAGGT,TGGGTGGGAGGGAGAGAGGT,TGGGAGAGAGGGAGAGAGGT 2.42927 . ANN=TGGGGGGGAGGGAGAGAGGT|splice_region_variant&intron_variant|LOW|SH2D5|SH2D5|transcript|NM_001103161.2|protein_coding|5/9|...||||||||||||||||||||||||||;dbNSFP_ada_score=1.43020658327008E-4,0.00157457299236331,5.16496450143413E-5;dbNSFP_rf_score=0.016,0.054,0.0;dbNSFP_PHRED=5.632,0.077,6.365,7.459,2.716
dbNSFP_ada_score is an ensemble prediction score, as calculated by dbNSFP.
