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Old 01-05-2012, 04:27 AM   #1
amruta.bn
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Exclamation 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?
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Old 01-05-2012, 06:06 AM   #2
adaptivegenome
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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.
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Old 01-12-2012, 02:42 AM   #3
amruta.bn
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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
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Old 05-29-2012, 08:42 PM   #4
yumtaoist
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Quote:
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
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