Dear helper, I used samtools and bcftools to get the SNP. However, I used the same Bam file and the same procedures to run samtools and bcftools with different versions. The results are different. What I did is the following.
Version 1.0 samtools mpileup -t DP -ugf fasta_file bam_file > output_mpileup bcftools call output_mpileup -vmO v -o output_call The output_call that I got is around 10 SNPs. Version 1.3.1 samtools mpileup -t DP -ugf fasta_file bam_file > output_mpileup bcftools call output_mpileup -vmO v -o output_call The output_call that I got is around 320 SNPs. Did you meet the same situation before? Is there any idea about that? Thank you. Best regards, Silas ------------------------------------------------------------------------------ What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
