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  1. UGENE
  2. UGENE-1619

"Call variants" pipeline's result are different from console launch when -P is used

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    Details

    • Tests Type:
      Functional/Unit
    • Affect Type:
      Userdefined

      Description

      These strings were used for console launch:
      samtools mpileup -uf /test/_common_data/NIAID_pipelines/Call_variants/input_data/dengue/dengue3.fasta /test/_common_data/NIAID_pipelines/Call_variants/input_data/dengue/dengue_sorted.bam | bcftools view -bvcg - > var.raw.bcf

      bcftools view -P cond2 var.raw.bcf > /your/output.vcf

      Console output differs from UGENE output(first diff is in line 17 of UGENE output)

        Attachments

          Issue Links

          relates to

          Improvement - An improvement or enhancement to an existing feature or task. UGENE-1043 VCF full support

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. UGENE-1477 VCF Format doesn't support comments and headers

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. UGENE-1043 VCF full support

          • Major - Major loss of function.
          • Closed

            Activity

              People

              Assignee:
              ggrekhov German Grekhov
              Reporter:
              vmalin Vladimir Malinovskiy
              Assigned Tester:
              Vladimir Malinovskiy
              Watchers:
              1 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: