Tweet
Hi everyone
I have one question about FreeBayes.
I'm trying to call SNP from haploid genome with the follow lines:
------------------------------------------------------------------------------------------------------------------------
samtools faidx ref.fasta (index fasta reference)
samtools view -bt ref.fasta.fai aln.sam > aln.bam (convert bowtie2 alignment *.sam file to bam)
samtools sort aln.bam aln.sorted (apply sort)
samtools calmd -Abr aln.sorted.bam ref.fasta > aln.baq.bam
samtools index aln.baq.bam (index bam files)
freebayes --min-base-quality 20 -p 1 --fasta-reference ref.fasta aln.baq.bam > aln.vcf (create the VCF file)
bcftools view -D -1 -Sb aln.vcf > aln.bcf (convert VCF to BCF)
samtools mpileup -uf ref.fasta aln.baq.bam | bcftools view -vcg -S aln.vcf - | perl vcfutils.pl vcf2fq > aln.consensus.fq (create a consensus sequence with SNPs)
------------------------------------------------------------------------------------------------------------------------
The problem is:
The file aln.consensus.fq do not show all the bases that match to reference sequence. Instead it, the fq file just show the SNPs between "n" like this: nnnnnnncnnnnnannnnttnnnnnnnnnannnnn.
Someone can help me to solve this?
Thanks
I have one question about FreeBayes.
I'm trying to call SNP from haploid genome with the follow lines:
------------------------------------------------------------------------------------------------------------------------
samtools faidx ref.fasta (index fasta reference)
samtools view -bt ref.fasta.fai aln.sam > aln.bam (convert bowtie2 alignment *.sam file to bam)
samtools sort aln.bam aln.sorted (apply sort)
samtools calmd -Abr aln.sorted.bam ref.fasta > aln.baq.bam
samtools index aln.baq.bam (index bam files)
freebayes --min-base-quality 20 -p 1 --fasta-reference ref.fasta aln.baq.bam > aln.vcf (create the VCF file)
bcftools view -D -1 -Sb aln.vcf > aln.bcf (convert VCF to BCF)
samtools mpileup -uf ref.fasta aln.baq.bam | bcftools view -vcg -S aln.vcf - | perl vcfutils.pl vcf2fq > aln.consensus.fq (create a consensus sequence with SNPs)
------------------------------------------------------------------------------------------------------------------------
The problem is:
The file aln.consensus.fq do not show all the bases that match to reference sequence. Instead it, the fq file just show the SNPs between "n" like this: nnnnnnncnnnnnannnnttnnnnnnnnnannnnn.
Someone can help me to solve this?
Thanks