Question: Pileup Haploid Base Calling, Creating Consensus Sequence
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gravatar for Lee Katz
7.1 years ago by
Lee Katz2.9k
Atlanta, GA
Lee Katz2.9k wrote:

Hi all, I couldn't find if this has been asked here. I realize that samtools assumes that you are working with a diploid and will output heterozygous snps. How could I modify my script to make it not output heterozygous snps? In other words, how do I trick it into thinking that it is looking at a haploid genome? My snippet of code is in Perl and uses a command() subroutine which runs a string and prints the command to the screen.

command("samtools mpileup -uf $$settings{assembly} $bam > $out1");
command("bcftools view -cg - < $out1 > $out2");
command("vcfutils.pl vcf2fq -d $minDepth -D $maxDepth < $out2 > $fastqOutNonstandard");
command("vcfutils.pl varFilter -d $minDepth -D $maxDepth < $out2 > $variantsFile");
samtools pileup • 2.1k views
ADD COMMENTlink written 7.1 years ago by Lee Katz2.9k

Is there perhaps something like GATK which could do it instead?

ADD REPLYlink written 7.1 years ago by Lee Katz2.9k
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