How To Extract All Alleles For A Specific Location From A Bam/ Sam Files?

Question

[Mpiro]

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.

Answer 1

[Pierre Lindenbaum]

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

http://samtools.sourceforge.net/

Answer 2

[Pirooz1]

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[?]