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Old 08-24-2011, 06:07 AM   #1
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Location: South Africa

Join Date: Apr 2011
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Default Generating vcf files with samtools

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 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 ( varFilter -D 500 vcf_sample > vcf_filtered_sample) does.

Any help or suggested reading would be much appreciated!
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Old 06-05-2012, 11:41 PM   #2
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Location: india

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The ID column represents the ID of dbsnp database, i.e if the variant is reported in dbsnp then its ID will be given there, and u can reduce the read depth by setting the option -D 10 in vcfutils command.
vcfutil command converts the binary file bcf to a more readable format of variants and also we can use various filters to get more novel variants
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