Tag: samblaster

Paired-end reads reported without mates: how to play matchmaker?

Hi Everyone, I am currently looking at Acute Myeloid Leukemia (AML) paired-end WGS samples from the TARGET data ocg.cancer.gov/programs/target/target-methods#3241. A bioinformatician in our group remapped the samples from hg19 to hg38. Unfortunately, we do not have any copies of the hg19 version anymore. However, when I try to run anything…

Continue Reading Paired-end reads reported without mates: how to play matchmaker?

Error in pipe output to samblaster from bwa-mem2

Error in pipe output to samblaster from bwa-mem2 0 Hi, I am trying to upgrade my command from bwa to bwa-mem2. This command usually works. bwa mem -M -R “@RGtID:idtSM:sampletLB:lib” human_g1k_v37.fasta sample.1.fq sample.2.fq | samblaster -M –excludeDups –addMateTags –maxSplitCount 2 –minNonOverlap 20 | samtools view -S -b – > sample.bam…

Continue Reading Error in pipe output to samblaster from bwa-mem2