Hello,
for getting a sorted bam file out of an unsorted sam file i often found these commands:
My questions are:
1. When do I need to give the reference file as an argument?
2. Are there any disadvantages if I do this:
fin swimmer
for getting a sorted bam file out of an unsorted sam file i often found these commands:
Code:
samtools view -bS file.sam | samtools sort - > file_sorted.bam samtools view -bT reference.fa file.sam | samtools sort - > file_sorted.bam
1. When do I need to give the reference file as an argument?
2. Are there any disadvantages if I do this:
Code:
samtools sort -O BAM file.sam > file_sorted.bam
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