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  • Is SRA format to vcf conversion possible

    Hi,

    I am new to SRA format. Can anyone give me an introduction.
    I wanted to convert SRA format to vcf format.
    I have checked in SRAToolkit. It does not support direct conversion of SRA to VCF. One option i am having is that first i have to convert to fastaq and then to SAM/BAM and then i should call variants.

    Can anyone please help me?

  • #2
    This is correct. The SRA data is converted to FASTQ. Then you must map the FASTQ data to a reference genome and once you have done this, you can generate a VCF using a variant caller.

    Comment


    • #3
      Hi,

      I generated the SAM file using bowtie version0.12.7 but i am not able to generate a proper bcf file.BCF file is genertaed within 2 minutes and normally it will take time.The commands i gave is

      time ./fastq-dump SRR068289.sra

      I have falidated the fastaq using fastaqvalidator and it was successful


      time ./bowtie -k 2 -v 2 hg19 -q /store/data/amruta/sratoolkit.2.1.8-centos_linux64/12JAN/SRR068289.fastq -S > /store/data/amruta/sratoolkit.2.1.8-centos_linux64/12JAN/bowtie1-amruta.sam

      From sam file bam was generated and using samtools bcf and vcf were generated
      ./samtools view -bS bowtie1-amruta.sam > bowtie1-amruta.sam
      my.flt.vcf
      samtools sort filename.bam sorted
      samtools faidx input.reference.fa
      samtools index sortedhg19.bam
      samtools mpileup -d 8000 -uf input.reference.fa my.sortedhg19.bam | bcftools view -bvcg -> my.raw.bcf
      bcftools view my.raw.bcf | perl vcfutils.pl varFilter -D8000 > my.flt.vcf

      My fastaq file is a huge in size.So i tried with bowtie 2 beta version.But i am not able to run bowtie2

      ./bowtie2 -x hg19 -u file.fataq -S out.sam

      The error was "Error: Encountered internal Bowtie 2 exception (#1)"
      Can anyone please help

      Comment


      • #4
        Originally posted by amruta.bn View Post
        Hi,

        I generated the SAM file using bowtie version0.12.7 but i am not able to generate a proper bcf file.BCF file is genertaed within 2 minutes and normally it will take time.The commands i gave is

        time ./fastq-dump SRR068289.sra

        I have falidated the fastaq using fastaqvalidator and it was successful


        time ./bowtie -k 2 -v 2 hg19 -q /store/data/amruta/sratoolkit.2.1.8-centos_linux64/12JAN/SRR068289.fastq -S > /store/data/amruta/sratoolkit.2.1.8-centos_linux64/12JAN/bowtie1-amruta.sam

        From sam file bam was generated and using samtools bcf and vcf were generated
        ./samtools view -bS bowtie1-amruta.sam > bowtie1-amruta.sam
        my.flt.vcf
        samtools sort filename.bam sorted
        samtools faidx input.reference.fa
        samtools index sortedhg19.bam
        samtools mpileup -d 8000 -uf input.reference.fa my.sortedhg19.bam | bcftools view -bvcg -> my.raw.bcf
        bcftools view my.raw.bcf | perl vcfutils.pl varFilter -D8000 > my.flt.vcf

        My fastaq file is a huge in size.So i tried with bowtie 2 beta version.But i am not able to run bowtie2

        ./bowtie2 -x hg19 -u file.fataq -S out.sam

        The error was "Error: Encountered internal Bowtie 2 exception (#1)"
        Can anyone please help
        Perhaps the new version of bowtie2 can run successfullly

        Comment

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