Downsampling Bam with samtools
samtools view [option] [sample.bam]
출처:https://www.htslib.org/doc/samtools-view.html
samtools-view(1) manual page
Manual page from samtools-1.18 released on 25 July 2023 samtools view – views and converts SAM/BAM/CRAM files samtools view [options] in.sam|in.bam|in.cram [region...] With no options or regions specified, prints all alignments in the specified input ali
www.htslib.org
Baseline command
#25% subsampling
samtools view -s 0.25 -b sample.bam > 25p_sample.bam
#50% subsampling
samtools view -s 0.5 -b sample.bam > 50p_sample.bam
#75% subsampling
samtools view -s 0.75 -b sample.bam > 75p_sample.bam
Downsampling specific region (ChrX only)
samtools view -bh sample.bam chrX > only_chrX.bam
samtools view -s 0.50 -b only_chrX.bam > 50p_chrX.bam
#합쳐주기
#samtools merge result_50p_chrX.bam -b exclude_chrX.bam 50p_chrX.bam
#samtools index result_50p_chrX.bam
samtools-merge(1) manual page
Manual page from samtools-1.18 released on 25 July 2023 samtools merge – merges multiple sorted files into a single file samtools merge [options] -o out.bam [options] in1.bam ... inN.bam samtools merge [options] out.bam in1.bam ... inN.bam Merge multiple
www.htslib.org
출처:https://www.htslib.org/doc/samtools-merge.html
samtools-index(1) manual page
Manual page from samtools-1.18 released on 25 July 2023 samtools index – indexes SAM/BAM/CRAM files samtools index -M [-bc] [-m INT] FILE FILE [FILE...] samtools index [-bc] [-m INT] aln.sam|aln.bam|aln.cram [out.index] Index coordinate-sorted BGZIP-comp
www.htslib.org
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