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I am wondering if anyone has tried popbam? I am looking for software to conduct population-level analyses, e.g., to compute nucleotide diversity, SNPs, and export alignments of particular genes to population genetics software. I have ~100 candidate genes I want to pull from a larger BAM file (454 reads aligned with Mosaik) for more in-depth analyses. I tried popbam, which appears to run, but doesn’t give any output. E.g., the command:
popbam snp –f reffile.fasta mysamples.bam
appears to run, but no output in the terminal or in the working directory. No error messages given. Bam and reference are indexed and sorted and both files are recognized by other packages such as samtools.
My three questions are (1) has anyone used popbam, (2) what does it give you for output (e.g., .vcf for snps), and (3) are there comparable packages that do similar analyses with next-gen data? I am aware of the wide array of SNP callers. Thanks!
popbam snp –f reffile.fasta mysamples.bam
appears to run, but no output in the terminal or in the working directory. No error messages given. Bam and reference are indexed and sorted and both files are recognized by other packages such as samtools.
My three questions are (1) has anyone used popbam, (2) what does it give you for output (e.g., .vcf for snps), and (3) are there comparable packages that do similar analyses with next-gen data? I am aware of the wide array of SNP callers. Thanks!
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