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  • #16
    We are having the same problem with 2.3.5

    <pre>#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1
    chr1 6529182 . TTCC TCC . PASS ADP=314;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDPP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:255:322:314:178:138:43.67%:1.1101E-50:34:31:88:90:70:68</pre>

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    • #17
      Originally posted by eeyun View Post
      We are having the same problem with 2.3.5

      <pre>#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1
      chr1 6529182 . TTCC TCC . PASS ADP=314;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDPP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:255:322:314:178:138:43.67%:1.1101E-50:34:31:88:90:70:68</pre>
      As far as I can tell, it should be ref = TTCC and alt = T

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      • #18
        Originally posted by eeyun View Post
        As far as I can tell, it should be ref = TTCC and alt = T
        Attachment included here to show the variant in question.
        Attached Files

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        • #19
          solved indel vcf format with awk command

          Here is an awk command that can change your indel vcf format into the correct format.

          cat Original_VCF | awk 'BEGIN {OFS="\t"} NR <= 24' > FINAL_VCF && cat Original_VCF | awk 'BEGIN {OFS="\t"} NR >= 25 { if (length($4)>length($5)) {$5 = substr($4, 0, 1)}; print }' >> FINAL_VCF


          It uses two awk commands because the second command changes the header of the file if you run it on the whole file. So the first awk command transfers the header(assumed to be 24 lines) and then from the 25th line down is the vcf indels that are changed to the correct indel format using the second awk command.

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          • #20
            I am also facing the +/- issue in the varscan indel notations - however i do not use the vcf output but prefer the regular tabular output of Varscan. Is there a way that this indel notation can be changed so as to be compatible with annovar ? I use Varscan 2.3.6

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            • #21
              I'm also seeing the slashes with VarScan v2.3.6
              I wrote this script to convert the slashes to commas:

              Code:
              import sys
              
              if len(sys.argv) < 2:  sys.exit("Usage: " + sys.argv[0] + "  vcf_filename")
              
              in_fname = sys.argv[1]
              out_fname = (in_fname[:-4] if in_fname.endswith(".vcf") else in_frame) + ".fixed.vcf"
              print("Writing to: " + out_fname)
              out = open(out_fname, "w")
              for line in open(in_fname):
                      if not line or line[0] is "#":
                              out.write(line)
                      else:
                              fields = line.split("\t")
                              fields[3] = fields[3].replace("/", ",").replace("\\", ",")   # remove any slashes from REF field
                              fields[4] = fields[4].replace("/", ",").replace("\\", ",")   # remove any slashes from ALT field
                              out.write("\t".join(fields))
              To use, just copy-paste into a file (lets say script.py) and run:

              python script.py file.vcf


              Also, this version of the script just removes the vcf records with slashes:

              Code:
              import sys
              
              if len(sys.argv) < 2:  sys.exit("Usage: " + sys.argv[0] + "  vcf_filename")
              
              in_fname = sys.argv[1]
              out_fname = (in_fname[:-4] if in_fname.endswith(".vcf") else in_frame) + ".fixed.vcf"
              print("Writing to: " + out_fname)
              out = open(out_fname, "w")
              for line in open(in_fname):
                      if not line or line[0] is "#":
                              out.write(line)
                      else:
                              fields = line.split("\t")
                              if "\\" not in (fields[3]+fields[4]) and "/" not in (fields[3]+fields[4]):
                                      out.write("\t".join(fields))
              Last edited by bw.; 02-05-2014, 02:16 PM. Reason: Turns out slashes also sometimes appear in the REF field, so added checks for that.

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              • #22
                If you are using VarScan mpileup2snp or mpileup2indel, why does the QUAL column not have a number in it?

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                • #23
                  Varscan vcf output for indel

                  Hi,

                  I am also encountering issues with vcf output of indels. I have got indels that look like this:

                  1 984171 . CAG AG .
                  1 1588744 . AGCG GCG .

                  I checked genome browser for the context of both mutations(http://genome.ucsc.edu/cgi-bin/hgTra...A984170-984180 and http://genome.ucsc.edu/cgi-bin/hgTra...588740-1588750), it seems that the first one is supposed to be simple deletion of the first base and the should look like this:

                  1 984170 . GC G .

                  And the second one can be either represented by a block substitution that looks like this:

                  1 1588743 . AAG AG .

                  or a deletion (if you align the deletion to the left) that looks like this:

                  1 1588742 . GA G .

                  So I do not know whether I did something wrong or it was because Varscan has a different vcf output format for indels?

                  Please help me. Many many thanks.

                  Comment

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