merge bam
I am trying to create a combined bam file, from 8 files, to view on IGV
I get this error
What I can do ?
base) [email protected] BWA % samtools merge -o merged.bam V350019555_L03_B5GHUMqcnrRAABA-549.bam V350019555_L03_B5GHUMqcnrRAABA-550.bam V350019555_L03_B5GHUMqcnrRAABA-551.bam V350019555_L03_B5GHUMqcnrRAAB(base) [email protected] BWA % samtools merge -o merged.bam V350019555_L03_B5GHUMqcnrRAABA-549.bam V350019555_L03_B5GHUMqcnrRAABA-550.bam V350019555_L03_B5GHUMqcnrR(base) [email protected] BWA % samtools merge -o merged.bam V350019555_L03_B5GHUMqcnrRAABA-549.bam V350019555_L03_B5GHUMqcnrRAABA-550.(base) [email protected] BWA % samtools merge -o merged.bam V350019555_L03_B5GHUMqcnrRAABA-549.bam V350019555_L03_B5GHUMqcnrRAABA-550.bam V350019555_L03_B5GHUMqcnrRAABA-551.bam V350019555_L03_B5GHUMqcnrRAABA-552.bam V350019555_L03_B5GHUMqcnrRAABA-553.bam V350019555_L03_B5GHUMqcnrRAABA-554.bam V350019555_L03_B5GHUMqcnrRAABA-555.bam V350019555_L03_B5GHUMqcnrRAABA-556.bam
samtools: invalid option -- o
the version es 1.3.1
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I guess the size increase because the output qualities are less homogenous, ie the number of different letters coded as qualities increased and hence it's "harder" to compress.
I guess such sequence is easier to compress:
",:,:,F,::F,,FFFF,,F,,,F:F::,F,F,F,F,F,FFF:,FF,F,:,:FF,F,F:FFFFFFFFF,FFFF:FFFFFF:FFFFFFFFFFFFFFFFFF,FF"
than
"/>-=-H'@>;/-BGCF-/B0.-F>[email protected]@.J-B0C-F/B0CFF?'GC-F/70>FF/[email protected]" like in my case after recalibration.Leave a comment:
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Perhaps this is applicable in your case as well: http://gatkforums.broadinstitute.org...-recalibrationLeave a comment:
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I haven't used it in forever but it may be keeping the old quality scores as well as the recalibrated ones. If that is default now there is an option to have it not do that (at least there was over a year ago when I last looked at this).Leave a comment:
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bam file increases in size following base recalibration
I am doing some whole genomes and after the alignments, I am doing the indel-realign and base reaclibration steps. I am seeing an odd result. The bam file after the base recalibration increases in size as below:
After the indel re-align, which is the same size as the originally mapped file:
114G Aug 23 08:51 Nrml_IndelRealin.bam
96G Aug 23 21:59 umr_IndelRealin.bam
After base quality recalibration:
126G Aug 25 20:40 Nrml_IndelRealin.BQSR.bam
127G Aug 25 15:44 Tumr_IndelRealin.BQSR.bam
Is this normal? Should the file size increase?
Thanks
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Targeted sequencing is an effective way to sequence and analyze specific genomic regions of interest. This method enables researchers to focus their efforts on their desired targets, as opposed to other methods like whole genome sequencing that involve the sequencing of total DNA. Utilizing targeted sequencing is an attractive option for many researchers because it is often faster, more cost-effective, and only generates applicable data. While there are many approaches...03-10-2023, 05:31 AM
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