I performed an experiment to track mutation accumulation over time in a fungal population. I sequenced several individual genomes from different time points and would like to extract the SNP sites only.
I currently have transformed my raw reads into *.sorted.bam files. I would like to use mpileup without a reference .fasta file because I'm only interested in the SNPs among *my* genomes, not between my genomes and the published reference genome. Is this possible?
When I use the following commands without a supplied "-f ref.fasta" switch:
I get zero SNPs in the .vcf file, though the .bcf file is enormous.
When I use the commands:
I get 1700 SNPs in the .vcf, and the .bcf is much smaller than the no_ref.bcf file.
Does anyone have any idea what is causing the discrepancy here? I would expect to find more SNPs between my samples and the reference.fasta than I would just among my samples, which are all related.
Thank you!
I currently have transformed my raw reads into *.sorted.bam files. I would like to use mpileup without a reference .fasta file because I'm only interested in the SNPs among *my* genomes, not between my genomes and the published reference genome. Is this possible?
When I use the following commands without a supplied "-f ref.fasta" switch:
samtools mpileup -ug sorted.bam1..3 | bcftools view -bcvg - > mpileup_noref.bcf
bcftools view mpileup_noref.bcf | vcfutils varFilter > mpileup_noref.vcf
bcftools view mpileup_noref.bcf | vcfutils varFilter > mpileup_noref.vcf
I get zero SNPs in the .vcf file, though the .bcf file is enormous.
When I use the commands:
samtools mpileup -ugf ref.fasta sorted.bam1..3 | bcftools view -bcvg - > mpileup_ref.bcf
bcftools view mpileup_ref.bcf | vcfutils varFilter > mpileup_ref.vcf
bcftools view mpileup_ref.bcf | vcfutils varFilter > mpileup_ref.vcf
I get 1700 SNPs in the .vcf, and the .bcf is much smaller than the no_ref.bcf file.
Does anyone have any idea what is causing the discrepancy here? I would expect to find more SNPs between my samples and the reference.fasta than I would just among my samples, which are all related.
Thank you!
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