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The total size of the bam file outputted by methphaser has decreased.
My bam size after Whatshap processing is 175 G, but the total size of the bam after methphaser processing is 142 G.
175G Nov 30 01:33 HG002_ONT_md_sup.whatshap.haplotag.bam
total 142G
6.7G Dec 1 15:20 output_ob.10.methtagged.bam
6.8G Dec 1 15:47 output_ob.11.methtagged.bam
6.8G Dec 1 15:28 output_ob.12.methtagged.bam
4.8G Dec 1 15:25 output_ob.13.methtagged.bam
4.6G Dec 1 15:53 output_ob.14.methtagged.bam
4.2G Dec 1 14:55 output_ob.15.methtagged.bam
4.4G Dec 1 14:58 output_ob.16.methtagged.bam
4.2G Dec 1 14:56 output_ob.17.methtagged.bam
3.8G Dec 1 15:23 output_ob.18.methtagged.bam
3.0G Dec 1 14:42 output_ob.19.methtagged.bam
12G Dec 1 16:02 output_ob.1.methtagged.bam
3.1G Dec 1 14:44 output_ob.20.methtagged.bam
2.0G Dec 1 14:38 output_ob.21.methtagged.bam
1.9G Dec 1 15:20 output_ob.22.methtagged.bam
12G Dec 1 15:59 output_ob.2.methtagged.bam
9.9G Dec 1 15:54 output_ob.3.methtagged.bam
9.4G Dec 1 15:52 output_ob.4.methtagged.bam
9.0G Dec 1 15:44 output_ob.5.methtagged.bam
8.6G Dec 1 15:42 output_ob.6.methtagged.bam
7.9G Dec 1 15:52 output_ob.7.methtagged.bam
7.3G Dec 1 15:37 output_ob.8.methtagged.bam
5.9G Dec 1 15:16 output_ob.9.methtagged.bam
3.9G Dec 1 15:10 output_ob.X.methtagged.bam
489M Dec 1 15:27 output_ob.Y.methtagged.bam
This is how i run mathphaser :
meth_phaser_parallel -b HG002_ONT_md_sup.whatshap.haplotag.bam -r hs37d5.fa -g whatshap_hg02.gtf -vc whatshap_hg02.vcf.gz -o work -t 16
meth_phaser_post_processing -ib HG002_ONT_md_sup.whatshap.haplotag.bam -if work/ -ov output.vcf -ob output_ob -vc whatshap_hg02.vcf.gz -t 16
What is the reason of the problem?How can i solve it?
Thanks!
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