I newly learn bioinformatics, and I want to develop a certain program,
1) open BAM file in Java program
2) want to find some reads, through embedded 'samtools mpileup' with some option, selected loci.
is it possible?
if it is possible, please tell me what should i do.
my ideal is, Get the 'samtools mpileup' source code,
and directly plus to java program code. but i can't find mpileup code.
•
written
by
Peavil •
is it possible?
yes
if it is possible, please tell me what should i do.
samtools mpileup [-EBugp] [-C capQcoef] [-r reg] [-f in.fa] [-l list] [-Q minBaseQ] [-q minMapQ] in.bam [in2.bam [...]]
i know… samtools mpileup has many options,
1) SamLocusIterator has same optional functions?
if not,
2) if it is developed, i should learn mpileup processing?
I don’t understand whole process NGS, sorry for weird question. and thank you very much for your comment
If you need mpileup, can can just call 'mpileup' from java with a system call. What is your actual biological goal?
I am trying to develop qc tool on selected loci reads,
i thought using system call is easy way,
but my boss want built-in one program
serviced for not IT based people.
no complex install, no long command... just like FastQC tool.
mpileup -> calling variant -> analysis for QC
I am trying to develop qc tool on selected loci reads,
why do you need mpileup ?
Extract reads from bam by predefined loci
this is not what mpileup does. Mpileup extract the number of reads and their qualities for each positions.
what you are looking looks more like samtools view and again, you can use a SamReader to get the reads in a defined region: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SamReader.html#query-java.lang.String-int-int-boolean-
but my boss want built-in one program serviced for not IT based people.
fastqc is a bash script calling java with a few distinct jar files.
why can't you call a C program from java ?
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