More posts like this
-
Installing ensemble VEP by running INSTALL.pl takes too long.
written by lsy9 •How long does it usually take to install Ensembl VEP with INSTALL.pl? I am running INSTALL.pl and I think it's taking too long. I am …
-
samtools mpileup error - 1 samples in 1 input files
written by joseph.kelly.94 •Hi All, I have relatively new to bioinformatics and have encountered an issue when trying to generate an mpileup file with samtools. I have entered …
-
samtools mpileup fail to create bcf
written by mthm •I have indexed my reference.fasta using bowtie2: bowtie2-build reference.fasta reference.fasta created the bam file form the sam file using samtools, sorted and indexed the bam …
-
Running Mpileup on a list of SNP regions
written by AK2019 •Hello! Budding bioinformaticion here so please bear with me here.. I am trying to run mpileup on a bed file (chrX start stop) that contains …
-
Error in bcftools view -bvcg command
written by hafiz.talhamalikI am using this pipeline to make a vcf file. but m having problem at step 4. `bcftools view -bvcg my-raw.bcf > my-var.bcf` it says …
-
Samtools mpileup taking a long time to finish
written by williamsbrian5064Hi, I am using samtools for variant calling. The issue I am having is that samtools mpileup seems to be taking a very long time. …
-
My VCF files are of zero length?
written by mahnoornaseer97 •i have sorted bam files , i used these command to generate VCF file but my file only has headers, it does not show any …
-
BCF file is too big? (from 3,73 GB sorted.bam file to over 200 GB BCF)
written by Clark_BioMorgan •I Have a sorted BAM file which is 3,73 GB in size and I use this command; $ samtools mpileup -u -f wholegenome.fa oz.sorted.bam > …
-
Denovogear Support Marked Dup And Sorted Bam Files?
written by kulkarni.aishwarya87 •<p>Does denovogear support marked dup and sorted <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> files? I was trying to run the bcf file generated from mpileup command on the marked …
-
Generating Both Pileup And Vcf/Bcf Using Samtools Mpileup
written by claresloggett •<p>I'm using <a href='http://samtools.sourceforge.net/'>samtools</a> mpileup and would like to generate both a pileup file and a vcf file as output. I can see how to …
The size shouldn't differ between sorted and unsorted files.
Maybe this is sam file? and what you're refering as sorted bam is bam file. But, 30Gb sam should be compressed to a smaller file than 18Gb.
I suggest you post the commands you used as well as the what you're sequencing.
Not quite. Sorted BAM files may have similar elements closer so they compress better. e.g. Size of BAM file reduces after sorting with samtools
Huh, does this happens with merged bams?
Now I think about it, I never written down an unsorted bam to notice the difference between sorted/unsorted file sizes and just assumed they would be similiar.
Bad assumtion :/, thanks for correcting.
My sam file is 126 gb
It can be slow, but I don't have an exact time. It's easy for you to get this though and it'd be more accurate than anything people here can give you as hardware differs. Index it and time it on a smaller region. Extrapolate from there.
A few pointers though.
bcftools mpileupinstead.-X. This can dramatically improve indel calling recall and precision.parallelto process each region and spit out a new file. You can then justbcftools concatthese together in order to get the final mpileup.