Originally posted by 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 helpLeave a comment:
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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.Leave a comment:
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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?
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