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Posts by flystar233
... First , samtools view -Sb sample.sam >sample.bam Second, samtools view sample.bam >sample2.sam I used this method: sam2bam2sam found that the head of the original sam file was lost at the end. So was it lost in sam2bam or bam2sam? ps：sample.sam have header information，sample2.sam ...
Comment: C: bwa mem -R or samtools -T
... oh，sorry，please see code： samtools view -SbT genome.fa sample.bam >uniq.bam - ...
... As we all know， bam file required by GATK need header in it. We can explicitly add it via the -R parameter.But，if you didn't use -R ,you also can use samtools -T genome.fa to add header. What is the difference between the two? ...
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