Question: How To Extract All Alleles For A Specific Location From A Bam/ Sam Files?
gravatar for Mpiro
8.9 years ago by
Mpiro10 wrote:

I need to know a specific location's allele from a bam file to find out if It is homozygous or heterozygous alleles in that location. Appreciate your help.

allele bam sequencing • 2.8k views
ADD COMMENTlink written 8.9 years ago by Mpiro10
gravatar for Pierre Lindenbaum
8.9 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum127k wrote:

BAM/SAM files describe the alignment of the short reads on the reference. There is no statistics about the probability Zygosity of the allele here.

However, using samtools view, you can visualize your reads at a given position or extract the zygosity of your mutation using samtools pileup

ADD COMMENTlink written 8.9 years ago by Pierre Lindenbaum127k
gravatar for Pirooz1
8.9 years ago by
Pirooz110 wrote:

GATK UnifiedGenotyper with genotype option can generate it:

java -Xmx4000m [?] -jar $gatk <br> -R $REF <br> -T UnifiedGenotyper <br> -I subject.bam <br> --DBSNP $DBSNP <br> --out snps.vcf <br> -stand_call_conf 30.0 <br> -stand_emit_conf 10.0 <br> -l INFO <br> -A HaplotypeScore <br> -L $ExonFile <br> -U ALLOW_UNINDEXED_BAM <br> --genotype[?]

ADD COMMENTlink written 8.9 years ago by Pirooz110
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