Hi, I am upgrading an analysis from samtools version 0.1.19-44428cd to version 1.3.1 (using htslib 1.3.1). I am trying to understand why the pileup changes so much in this example
samtools mpileup -s -f genomes/NC_000962.fna alignments/sample-1.bam | head [mpileup] 1 samples in 1 input files <mpileup> Set max per-file depth to 8000 NC_000962.3 1 T 13 ^],^],^],^],^],^].^].^].^].^].^].^],^], ;GF/GGGGGBCDH ]]]]]]]]]]]]] NC_000962.3 2 T 13 ,,,,,......,, ?GFF?GDGGBGGA ]]]]]]]]]]]]] NC_000962.3 3 G 13 ,,,,,......,, DGFFDGHGHFHGG ]]]]]]]]]]]]] NC_000962.3 4 A 13 ,,,,,......,, DGFFGGEGHAGGE ]]]]]]]]]]]]] NC_000962.3 5 C 13 ,,,,,......,, GGADDHDHHGHGE ]]]]]]]]]]]]] NC_000962.3 6 C 15 ,,,,,......,,^],^]. GGGBFHGHHGBGHFA ]]]]]]]]]]]]]]] NC_000962.3 7 G 15 ,,,,,......,,,. ;GFFGCGGGEGHHG3 ]]]]]]]]]]]]]]] NC_000962.3 8 A 15 ,,,,,......,,,. 0FGFG2GGGAGHGF> ]]]]]]]]]]]]]]] NC_000962.3 9 T 15 ,,,,,......,,,. CGGF0ECGGEGHCAA ]]]]]]]]]]]]]]] NC_000962.3 10 G 15 ,,,,,......,,,. ?GGFEEGGGECGG.A ]]]]]]]]]]]]]]] ./samtools-1.3.1/samtools mpileup -s -f genomes/NC_000962.fna alignments/sample-1.bam | head [mpileup] 1 samples in 1 input files <mpileup> Set max per-file depth to 8000 NC_000962.3 1 T 0 NC_000962.3 2 T 0 NC_000962.3 3 G 0 NC_000962.3 4 A 0 NC_000962.3 5 C 0 NC_000962.3 6 C 1 ^], A ] NC_000962.3 7 G 1 , 3 ] NC_000962.3 8 A 1 , > ] NC_000962.3 9 T 1 , A ] NC_000962.3 10 G 1 , A ] Is this change a change in the default settings somewhere such that the reads are filtered out? Thanks Adam ------------------------------------------------------------------------------ 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.http://sdm.link/zohodev2dev _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
