Specific output from bcftools, difference between DP4 and AC scores
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7.9 years ago
Lionir • 0

Hi all! I'm new to SNP calling, trying to call multisample data and output SNP counts for every of called SNPs. I use command

nohup samtools mpileup -t DP -vuf ~ref_genome *.bam  2> stderr.txt | bcftools call -A -m -Ov - > whole_data_called.vcf

To call all ALT snps. I got such output:

   1    10019   .   T   C,A 26.6345 .   DP=148;VDB=0.26;SGB=-0.453602;RPB=0.965753;MQB=0.965753;MQSB=0.999998;BQB=0.808219;MQ0F=0.966216;AC=0,0;AN=2;DP4=60,86,0,2;MQ=0 GT:PL:DP    0/0:0,255,62,255,65,62:148

So the questions are: 1. Is there any way to output every alternative SNP in new row to count SNP quality for every ALT allele without writing custom scripts? i.e. instead of row above get smth like this:

   1    10019   .   T   C   26.6345 .   INFO FIELD
   1    10019   .   T   A   26.6345 .   INFO FIELD

2. I've read VCF specification and got that DP4- filtered counts for reference and alternative allele. AC- counts for reference alleles. Why do I get DP4 in the example row above for alternative alleles 0,2 , when AC 0,0 indicates zeroes counts for every allele?

Thank you in advance.

SNP samtools bcftools • 2.3k views
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