how to seperate VEP INFO column into seperate columns

Question

[minoo]

I have a vcf files like below:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  treatmentSample
chr1    857100  .   C   T   1756.06 PASS    AC=2;AF=1;AN=2;DP=60;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=29.27;SOR=1.812;CSQ=chr1:857100|T|SNV|ENSG00000228794|ENST00000445118|LINC01128||1|MODIFIER|non_coding_transcript_exon_variant||||5/5|||||||||||||||||| GT:AD:DP:GQ:PL  1/1:0,60:60:99:1770,180,0

Does anyone know how to seperate INFO columns into different columns? And also how to separate treatmentSample column following the FORMAT ORDER? I TRIED TO USE bcftools +split-vep and awk but they didn't work.

bcftools +split-vep treatmentSample.vcf.gz -f '\t%CHROM\t%POS\t%ID\t%REF\t%ALT\t%QUAL\t%FILTER\t%FORMAT\t%treatmentSample\t%INFO\t% AC\t%AF\t%AN\t% MLEAC\t% MLEAF\t% MQ\t% QD\t%SOR\t%CSQ[\t%GT][\t%GQ][\t%DP][\t%MIN_DP][\t%AD][\t%VAF][\t%PL][\t%MED_DP]\n' -d -A tab > output.vcf

The output was like below:

Warning: duplicate INFO/CSQ key "CADD_phred"
Note: ambiguous key %AC; using the AC subfield of CSQ, not the INFO/AC tag
Note: ambiguous key %AN; using the AN subfield of CSQ, not the INFO/AN tag
Note: ambiguous key %Diag_Germline_Gene; using the Diag_Germline_Gene subfield of CSQ, not the INFO/Diag_Germline_Gene tag
Could not parse format string: \t%CHROM\t%POS\t%ID\t%REF\t%ALT\t%QUAL\t%FILTER\t%FORMAT\t%treatmentSample\t%INFO\t% AC\t%AF\t%AN\t% MLEAC\t% MLEAF\t% MQ\t% QD\t%SOR\t%Location %Allele %VARIANT_CLASS  %Gene   %Feature    %SYMBOL %CCDS   %STRAND %IMPACT %Consequence    %SIFT   %PolyPhen   %CADD_phred %EXON   %DISTANCE   %COSMIC_ID  %COSMIC_CNT %AC %AN %CADD_phred %gnomAD_exomes_AF   %gnomAD_exomes_NFE_AF   %ExAC_nonTCGA_AF    %ExAC_nonTCGA_NFE_AF    %gnomAD_genomes_AF  %gnomAD_genomes_NFE_AF  %phyloP100way_vertebrate    %clinvar_rs %clinvar_clnsig %clinvar_trait  %clinvar_golden_stars   %Diag_Germline_Gene[\t%GT][\t%GQ][\t%DP][\t%MIN_DP][\t%AD][\t%VAF][\t%PL][\t%MED_DP]\n

I need to be something like the below table:

#CHROM  POS ID  REF ALT QUAL    FILTER  AC  AF  AN  DP  ExcessHet   FS  MLEAC   MLEAF   MQ  QD  SOR Location    Allele  VARIANT_CLASS   Gene    Feature SYMBOL  CCDS    STRAND  IMPACT  Consequence SIFT    PolyPhen    CADD_phred  EXON    FORMAT  treatmentSample
chr1    857100  .   C   T   1756.06 PASS    2   1   2   60  30.103  0   2   1   60  29.27   1.812   chr1:857100 T   SNV ENSG00000228794 ENST00000445118 LINC01128       1   MODIFIER    non_coding_transcript_exon_variant              45051   GT:AD:DP:GQ:PL  0/1:39,11:50:99:172,0,1122

[Pierre Lindenbaum]

I TRIED TO USE bcftools +split-vep AND AWK BUT THEY DIDINT WORK.

read https://meta.stackexchange.com/questions/147616/

[minoo]

Right sorry I added the error.