User: devin.porter92

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Posts by devin.porter92

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Calling SNPs with low coverage
... Does anyone know of a program that can call SNPs with low coverage? I have been using samtools mpileup and bcftools/vcftools to find high confident SNPs. I am now trying to identify unknown samples based off of the reference SNP panel I generated. Therefore, I don't need high confidence in callin ...
vcf low-coverage samtools mpileup snp written 7 months ago by devin.porter920 • updated 9 days ago by pierre.peterlongo630
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Filtering multisample vcf file by
... Hello, I have a vcf file that contains 200 DO mouse samples. I want to filter the file by SNPs that have at least 5 of each genotype per SNP. Each SNP needs at least 5 AA, AB, and BB. For example, if a SNP has190 AA, 6 AB, and 4 BB then this would be discarded. Or if there are 100 AA, 0 AB, an ...
vcftools genotype written 8 months ago by devin.porter920 • updated 8 months ago by Pierre Lindenbaum101k
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Comment: C: bamtools filter specific motif sequence
... Thanks a lot! I was able to make it work with the following: samtools view -h input.bam | awk -F '\t' '($1 ~ /^@/ || $10 ~/AAACCTG/ )' >filter.sam ; samtools view filter.sam -Sb -o filter.bam ...
written 8 months ago by devin.porter920
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bamtools filter specific motif sequence
... I am trying to use bamtools filter to keep output a new bam file with a specific sequence. This is what I am using... bamtools filter -in Aligned.bam -queryBases AAACCTG >Aligned_1.bam This does not return any matches. The question I am asking, is it possible to filter sequencing reads from a B ...
filter motif bamtools written 8 months ago by devin.porter920 • updated 8 months ago by Pierre Lindenbaum101k

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