Demultiplexing bam file
Hi to everyone,
I have NIPT data from multiple samples which are sequenced by Iontorrent. All of them are aligned together using bowtie. I want to separate every sample from the aligned bam file which consists of all samples together. Part of the header of the bam file is:
@HD VN:1.4 GO:none SO:coordinate
@RG ID:QDQDB PL:IONTORRENT PU:s5/540/Q35S04/08/DAIL00351 FO:TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTG DT:2023-05-04T05:36:13-0300 SM:13.02.1402_POOL2 KS:TCAG CN:ParsGene/S5XL-GALAXY
@RG ID:QDQDB.1 PL:IONTORRENT PU:s5/540/Q35S04/08/DAIL00351 FO:TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTG DT:2023-05-04T05:50:01-0300 SM:13.02.1402_POOL2 KS:TCAG CN:ParsGene/S5XL-GALAXY
how can I do that?
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hasani.iut6
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I don't understand. In your header there is only one sample : "
13.02.1402_POOL2"so why the size of bam file is 40 gig?
you don't talk about the size in your question
Yes, you're right, I know the bam file consists of multiple samples (It should be between 30 to 40 samples) and the size of the bam file is about 45GIG.
So perhaps there are more samples.
hasani.iut6:
grep "SM*" header_of_bam. Is there more than one unique ID there?No. All of the Ids are "13.02.1402_POOL2". Do you think my bam file is not correct?