Hello all,
I have a segment from a yeast, and a yeast genome to compare it to. I want to get a list of SNPS, and eventually find a known SNP in the yeast sequence.
When I run this through bwa and samtools it seems to work fine up until its time for me to get the SNP list. When I use the pileup command I get empty files as output.
Here's what I'm running.
I made sure both my files have an equal line length, 80, formatted with fastx. Any insight would be very appreciated. Thanks so much!
I have a segment from a yeast, and a yeast genome to compare it to. I want to get a list of SNPS, and eventually find a known SNP in the yeast sequence.
When I run this through bwa and samtools it seems to work fine up until its time for me to get the SNP list. When I use the pileup command I get empty files as output.
Here's what I'm running.
Code:
#reference is yeast.nt #query is yeast.fasta bwa index /home/jill/bwa-0.5.8c/Project/yeast.fasta bwa index /home/jill/bwa-0.5.8c/Project/yeast.nt bwa aln /home/jill/bwa-0.5.8c/Project/yeast.nt /home/jill/bwa-0.5.8c/Project/yeast.fasta > /home/jill/bwa-0.5.8c/Project/yeastbwaout.sai #[bwa_aln] 17bp reads: max_diff = 2 #[bwa_aln] 38bp reads: max_diff = 3 #[bwa_aln] 64bp reads: max_diff = 4 #[bwa_aln] 93bp reads: max_diff = 5 #[bwa_aln] 124bp reads: max_diff = 6 #[bwa_aln] 157bp reads: max_diff = 7 #[bwa_aln] 190bp reads: max_diff = 8 #[bwa_aln] 225bp reads: max_diff = 9 #[bwa_aln_core] calculate SA coordinate... 0.15 sec #[bwa_aln_core] write to the disk... 0.00 sec #[bwa_aln_core] 1 sequences have been processed. bwa samse /home/jill/bwa-0.5.8c/Project/yeast.nt /home/jill/bwa-0.5.8c/Project/yeastbwaout.sai /home/jill/bwa-0.5.8c/Project/yeast.fasta > /home/jill/bwa-0.5.8c/Project/yeastbwaout.sam #[bwa_aln_core] convert to sequence coordinate... 0.01 sec #[bwa_aln_core] refine gapped alignments... 0.00 sec #[bwa_aln_core] print alignments... 0.01 sec #[bwa_aln_core] 1 sequences have been processed. samtools faidx /home/jill/bwa-0.5.8c/Project/yeast.nt samtools view -bt /home/jill/bwa-0.5.8c/Project/yeast.nt.fai /home/jill/bwa-0.5.8c/Project/yeastbwaout.sam > /home/jill/bwa-0.5.8c/Project/yeastbwaout.bam #[samopen] SAM header is present: 17 sequences. #index bam samtools index /home/jill/bwa-0.5.8c/Project/yeastbwaout.bam #Sorts bam samtools sort /home/jill/bwa-0.5.8c/Project/yeastbwaout.bam /home/jill/bwa-0.5.8c/Project/yeastbwaoutsort samtools index /home/jill/bwa-0.5.8c/Project/yeastbwaoutsort.bam samtools pileup -vcf /home/jill/bwa-0.5.8c/Project/yeast.nt.fai /home/jill/bwa-0.5.8c/Project/yeastbwaoutsort.bam | tee /home/jill/bwa-0.5.8c/Project/raw.txt | /home/jill/samtools-0.1.11/misc/samtools.pl varFilter -D100 > /home/jill/bwa-0.5.8c/Project/flt.txt awk '($3=="*"&&$6>=50)||($3!="*"&&$6>=20)' /home/jill/bwa-0.5.8c/Project/flt.txt > /home/jill/bwa-0.5.8c/Project/final.txt
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