User: fabiopertille

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Posts by fabiopertille

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Answer: C: How do I make a fasta reference file from a set of bam files in order to maximiz
... I figured out how to solve my problem. I was trying to generate a consensus from the merged file instead of considering all the individual genotypes separately to create the consensus. To figure out you can use *F1*_sorted.bam when I you create the vcf file as follow: samtools mpileup -uf gen ...
written 7 weeks ago by fabiopertille0
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Comment: C: How do I make a fasta reference file from a set of bam files in order to maximiz
... I am interested in the neighboring bases, I want to know if it is a CpG or CCpGG - SNP, this is why I have the coordinate of the SNPs neighbor bases. Looks you are providing a good tip, thank you, maybe with the consensus function I can define a criterion for calling heterozygous positions. However ...
written 7 weeks ago by fabiopertille0
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Comment: C: How do I make a fasta reference file from a set of bam files in order to maximiz
... Thanks for the help, but my concern is not exactly to find the correct name for the file I am currently calling "reference genome" of my bam files. I called like it to be easer to understand, sorry if it caused more confusion. And you are right, I am referring to a fasta consensus. My question is, h ...
written 7 weeks ago by fabiopertille0
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How do I make a fasta reference file from a set of bam files in order to maximize the number of heterozygotes in my reference genome?
... Through samtools, I merged all the .bam files that I wanted to be part of my reference genome. samtools merge F1.bam *F1*_sorted.bam I ordered and created the index of my bam file. samtools sort -m 768M F1.bam -o F1_sorted.bam samtools index F1_sorted.bam After that I created a fas ...
vcfutils samtools bcftools mpileup seqtk written 7 weeks ago by fabiopertille0 • updated 18 days ago by Biostar ♦♦ 20

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