Dear seq members
I am fairly new to SNP analysis. In my study, I have 2 groups, treatment and control, each containing 3 biological replicates. My goal is to find different snps between the two groups and I'm using samtools mpileup | bcftools in my analysis.
Shown below are my codes:
samtools mpileup -C 50 -uDS -q 10 -f MYPATH/human_ref_genome.fa output/tr1.bam output/tr2.bam output/tr3.bam output/ctr1.bam output/ctr2.bam output/ctr3.bam | bcftools view -bvcg - > ./snp_output/snp_cmp.bcf
bcftools view -c -1 -3 ./snp_output/snp_cmp.bcf | vcfutils.pl varFilter -D 100 > ./snp_output/snp_cmp.vcf
Did I use the correct command? Why did the output snp_cmp.vcf file contain millions of snps while I'm expecting hundreds of snps of interest? How did I only limit (filter) my scope to the different snps between the two groups and which program should I use to achieve this goal?
Thanks in advance.
I am fairly new to SNP analysis. In my study, I have 2 groups, treatment and control, each containing 3 biological replicates. My goal is to find different snps between the two groups and I'm using samtools mpileup | bcftools in my analysis.
Shown below are my codes:
samtools mpileup -C 50 -uDS -q 10 -f MYPATH/human_ref_genome.fa output/tr1.bam output/tr2.bam output/tr3.bam output/ctr1.bam output/ctr2.bam output/ctr3.bam | bcftools view -bvcg - > ./snp_output/snp_cmp.bcf
bcftools view -c -1 -3 ./snp_output/snp_cmp.bcf | vcfutils.pl varFilter -D 100 > ./snp_output/snp_cmp.vcf
Did I use the correct command? Why did the output snp_cmp.vcf file contain millions of snps while I'm expecting hundreds of snps of interest? How did I only limit (filter) my scope to the different snps between the two groups and which program should I use to achieve this goal?
Thanks in advance.
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