I am new to next gen sequence analysis and I was wondering if anyone could help me with some questions that I have regarding the use of SAMtools to generate vcf files:
I have used the following command lines to generate a vcf file:
samtools mpileup -gf GRCh37.fa sample.bam > mpileup_sample
bcftools view -bvcg mpileup_sample > bcf_sample
bcftools view bcf_sample > vcf_sample
vcfutils.pl varFilter -D 500 vcf_sample > vcf_filtered_sample
In the resulting vcf file, the columns "ID" and "FILTER" are empty, is there any way that I can obtain values for these columns?
Also, I would like to filter out all those samples that have a read depth less than 10 and Quality scores less than 20. Is there a way that I can do this in SAMtools?
Lastly, I am unclear as to what the last command line (vcfutils.pl varFilter -D 500 vcf_sample > vcf_filtered_sample) does.
Any help or suggested reading would be much appreciated!
I have used the following command lines to generate a vcf file:
samtools mpileup -gf GRCh37.fa sample.bam > mpileup_sample
bcftools view -bvcg mpileup_sample > bcf_sample
bcftools view bcf_sample > vcf_sample
vcfutils.pl varFilter -D 500 vcf_sample > vcf_filtered_sample
In the resulting vcf file, the columns "ID" and "FILTER" are empty, is there any way that I can obtain values for these columns?
Also, I would like to filter out all those samples that have a read depth less than 10 and Quality scores less than 20. Is there a way that I can do this in SAMtools?
Lastly, I am unclear as to what the last command line (vcfutils.pl varFilter -D 500 vcf_sample > vcf_filtered_sample) does.
Any help or suggested reading would be much appreciated!
Comment