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Old 09-09-2015, 01:56 AM   #1
Waqasuddin Khan
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Location: Karachi

Join Date: Nov 2013
Posts: 7
Default SNP at every chromosome position

Hi,

I SOLiD sequencing data. After aligning with SHRiMP2, I used samtools mpileup for SNP calling:

samtools mpileup -C50 -gf hg38.fa -o var.raw.bcf input.bam

bcftools call -o var.raw.vcf -O v -c var.raw.bcf

The raw vcf file looks like this:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SINDHI
chr1 33953 . T . 56.8087 PASS DP=11;MQSB=0.950952;MQ0F=1;AF1=0;AC1=0;DP4=6,5,0,0;MQ=0;FQ=-59.9998 GT:PL 0/0:0
chr1 33954 . C . 56.8087 PASS DP=11;MQSB=0.950952;MQ0F=1;AF1=0;AC1=0;DP4=6,5,0,0;MQ=0;FQ=-59.9998 GT:PL 0/0:0
chr1 33955 . T . 56.4609 PASS DP=10;MQSB=0.952347;MQ0F=1;AF1=0;AC1=0;DP4=5,5,0,0;MQ=0;FQ=-56.997 GT:PL 0/0:0
chr1 35396 . C . 56.4609 PASS DP=10;MQSB=0.952347;MQ0F=1;AF1=0;AC1=0;DP4=5,5,0,0;MQ=0;FQ=-56.997 GT:PL 0/0:0
chr1 35397 . C . 61.2368 PASS DP=12;MQSB=0.95494;MQ0F=1;AF1=0;AC1=0;DP4=5,7,0,0;MQ=0;FQ=-62.9905 GT:PL 0/0:0
chr1 35398 . C . 61.2368 PASS DP=12;MQSB=0.95494;MQ0F=1;AF1=0;AC1=0;DP4=5,7,0,0;MQ=0;FQ=-62.9905 GT:PL 0/0:0
chr1 35399 . A . 61.2368 PASS DP=12;MQSB=0.95494;MQ0F=1;AF1=0;AC1=0;DP4=5,7,0,0;MQ=0;FQ=-62.9905 GT:PL 0/0:0
chr1 35400 . A . 61.2368 PASS DP=12;MQSB=0.95494;MQ0F=1;AF1=0;AC1=0;DP4=5,7,0,0;MQ=0;FQ=-62.9905 GT:PL 0/0:0
chr1 35401 . C . 61.2368 PASS DP=12;MQSB=0.95494;MQ0F=1;AF1=0;AC1=0;DP4=5,7,0,0;MQ=0;FQ=-62.9905 GT:PL 0/0:0

As you can see, the chromosome position is continuous. I know that these are raw variant file but it contains 333,399,862 variants (almost as the number of bases). So, how can I filter this (there are so many false positives), i need filtration or should i do something at mpileup or bcftools call stage?
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Old 09-10-2015, 08:01 PM   #2
SNPsaurus
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You want to call -cv to display only the variant positions, instead of call -c which shows all positions. You can see in your vcf it lists ref bases without an alt, so the positions in your example would all be removed.
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