gravatar for khanhlpbao

2 hours ago by

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[[2]] : 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[[2]] : subscript out of bounds", anyone know what I should do to solve this problem?



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