indel detection

dindel

test mpileup
./samtools-bcftools-htslib-1.0_x64-linux/bin/samtools mpileup MM140738JS.bam -v -u > test.vcf
10:72358747

samtools mpileup -C50 -gf ref.fasta -r chr3:1,000-2,000 in1.bam in2.bam

./samtools-bcftools-htslib-1.0_x64-linux/bin/samtools mpileup -uf /lgc/datasets/hg19/new/hg19/hg19.fa MM140738JS.bam | ./samtools-bcftools-htslib-1.0_x64-linux/bin/bcftools call -mv > var.raw.vcf

http://gatkforums.broadinstitute.org/discussion/3255/indel-calling
https://www.broadinstitute.org/files/shared/mpg/nextgen2011/nextgen2011_delangel.pdf

GATK -glm INDEL

python /lgc/scripts/unifiergenotyper_indel.py -i MM140738JS.bam -t /lgc/datasets/sickkids/AmpliSeqExome.20131001.designed.bed -o MM140738JS.indel.vcf

grep “72358746” *.vcf [ 7:47AM]
raony@mendel{MM140738JS} grep “72358745” *.vcf [ 7:48AM]
MM140738JS.indel.vcf:chr10 72358745 . CA C 1049.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.769;DP=84;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=81.36;MQ0=0;MQRankSum=-1.613;QD=12.50;ReadPosRankSum=0.095 GT:AD:DP:GQ:PL 0/1:47,32:81:99:1087,0,1785

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