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  • Converter for vcf to bed format

    Hi all,

    Is there any converter that can convert vcf format files obtained by samtools vcfutils.pl to bed format?

    Because i want predict the variant effect using varian_effect_predictor of ensemble.

    ##fileformat=VCFv4.0
    #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT GKUNU9Q04_chr1_sort.bam
    chr1 46707 . A G 7.59 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=60 PL:GT:GQ 38,6,0:1/1:49
    chr1 168576 . C T 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=60 PL:GT:GQ 34,6,0:1/1:49
    chr1 168635 . G A 17.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=60 PL:GT:GQ 49,9,0:1/1:63

    To

    1 46707 46707 A/G +
    1 168576 168576 C/T +
    1 168635 168635 G/A +

  • #2
    The awesome power of awk and sed.

    Code:
    sed -e 's/chr//' file.vcf | awk '{OFS="\t"; if (!/^#/){print $1,$2-1,$2,$4"/"$5,"+"}}'
    where you replace "file.vcf" with your file. Note this uses 0-based start coordinates, which are the proper BED format. If you want to use 1-based, change "$2-1" to just "$2".

    Comment


    • #3
      Originally posted by quinlana View Post
      The awesome power of awk and sed.

      Code:
      sed -e 's/chr//' file.vcf | awk '{OFS="\t"; if (!/^#/){print $1,$2-1,$2,$4"/"$5,"+"}}'
      where you replace "file.vcf" with your file. Note this uses 0-based start coordinates, which are the proper BED format. If you want to use 1-based, change "$2-1" to just "$2".
      Thanks for reply,

      if suppose i want to put "-" reverse strand instead of "+", how can i put that using vcf file?

      1 46707 46707 A/G +
      1 168576 168576 C/T +
      1 168635 168635 G/A +
      1 195648 195648 T/G -

      Comment


      • #4
        GFF to BED

        How to convert a GFF file intO BED format file?.

        Comment


        • #5
          Maybe this will be useful?

          Comment

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