The command samtools fastq will directly convert a bam file to fastq files. Combining with the filter parameter, we could output unmapped read pairs by -f 12 . 0x0004 in the flag field of the SAM format means “the query sequence itself is unmapped” and 0x0008 & ...
Recently, I found that overlapping varaints existed in the results that called by GATK HaplotypeCaller (version 4.0.1.2). I noticed this because I want to build consensus sequences using bcftools consensus , which produced warnings like these: ThesiteChr01:597519  ...
Generally, for a program that support multi-threading, the elapsed time will reduce with the increasing number of used CPUs. However, I found a strang case that picard MarkDuplicates will run slower with more CPUs. When I run picard MarkDuplicates in a node with 160 CPUs, it ...