Converting Sam To Bam
I have set of sam files and I would like to convert them into bam files with the following script. But it didn't create bam files? What I have made wrong?
for file in `ls ~/wgs/sam`;
~/bin/samtools-0.1.18/samtools view -bS ~/wgs/sam/$file \
Haluk, you should use the option
-o FILE output file name [stdout] instead of redirecting the stdout to the bam file.
Not sure what you did wrong, but I use
samtools view -bT reference.fa test.sam > test.bam and it works pretty well
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