I’m trying to make the .bam file for analysis on NIPTeR. But now the file looks like having some problems I cannot understand. Bin_bam_sample always return “Error in splitted_reads[] : subscript out of bounds"
Here is method that I use:
Remove duplicates with fastp
Bwa aln follow with bwa samse
Convert .sam to .bam and only keep foward strand: samtools view -F 0x10 -bq 20 -S sample.sam.gz > sample.bam.gz
Samtools collate and samtools fixmate after that
Remove duplicate with GATK Picard
When run bin_bam_sample on that sample, it returned with "Error in splitted_reads[] : subscript out of bounds", anyone know what I should do to solve this problem?