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  • 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?

  • #2
    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.
    Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

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