Hi guys,
i have a question regarding annovar.
I have Torrent data which i have to map to 3 human genes only. I did that with BWA. After i had to do the annotation of SNPs. So i go to annovar. But somehow i get some weird results if any.
So i did so:
1. got the fasta seqs for the 3 genes and put them in a file together(3genes.fasta).
2. bwa index -a is 3genes.fasta
3. bwa aln - l 31 -k 2 -n 10 -t 4 3genes.fasta FILE.fastq > aln_sa.sai
4. bwa samse 3genes.fasta aln_sa.sai FILE.fastq > aln.sam
5. samtools faidx 3genes.fasta
6. samtools view -bt 3genes.fasta.fai -o aln.bam aln.sam
7. samtools sort aln.bam aln.bam.sorted
8. samtools mpileup -ugf 3genes.fasta aln.bam.sorted.bam |bcftools view -bvcg ->var.raw.bcf
9. bcftools view raw.vcf.bcf|vcfutils.pl varFilter -D 100 >var.flt.vcf
10. convert2annovar.pl var.flt.vcf -format vcf4 > var.flt.vcf.avinput
11. annotate_variation.pl -buildver hg19 var.flt.vcf.avinput /annovar/humandb/
12. annotate_variation.pl -buildver hg19 -filter -dbtype snp132 var.flt.vcf.avinput /annovar/humandb/
13. annotate_variation.pl -buildver hg19 var.flt.vcf.avinput.hg19_snp132_filtered /annovar/humandb/
Is it possible to use annovar in that way at all?
I am sorry if it seems a bit strange and not understandable but is difficult for me to explain. If any questions please ask.
thank you
i have a question regarding annovar.
I have Torrent data which i have to map to 3 human genes only. I did that with BWA. After i had to do the annotation of SNPs. So i go to annovar. But somehow i get some weird results if any.
So i did so:
1. got the fasta seqs for the 3 genes and put them in a file together(3genes.fasta).
2. bwa index -a is 3genes.fasta
3. bwa aln - l 31 -k 2 -n 10 -t 4 3genes.fasta FILE.fastq > aln_sa.sai
4. bwa samse 3genes.fasta aln_sa.sai FILE.fastq > aln.sam
5. samtools faidx 3genes.fasta
6. samtools view -bt 3genes.fasta.fai -o aln.bam aln.sam
7. samtools sort aln.bam aln.bam.sorted
8. samtools mpileup -ugf 3genes.fasta aln.bam.sorted.bam |bcftools view -bvcg ->var.raw.bcf
9. bcftools view raw.vcf.bcf|vcfutils.pl varFilter -D 100 >var.flt.vcf
10. convert2annovar.pl var.flt.vcf -format vcf4 > var.flt.vcf.avinput
11. annotate_variation.pl -buildver hg19 var.flt.vcf.avinput /annovar/humandb/
12. annotate_variation.pl -buildver hg19 -filter -dbtype snp132 var.flt.vcf.avinput /annovar/humandb/
13. annotate_variation.pl -buildver hg19 var.flt.vcf.avinput.hg19_snp132_filtered /annovar/humandb/
Is it possible to use annovar in that way at all?
I am sorry if it seems a bit strange and not understandable but is difficult for me to explain. If any questions please ask.
thank you
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