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Old 11-18-2013, 08:31 PM   #1
penolove
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Location: ROC

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Default how does insertion/deletion detected?

Excuse me,I'm new in this field, want to know how does deletion/insertions detected works in samtools.
Or any one have reference about deletion/insertions detected algorithm



Now I have a vcf file that


##reference=file:///lustre/scratch105/vrpipe/refs/human/ncbi37/human_g1k_v37.fasta
##source_20121105.1=vcf-annotate(r785) -f /nfs/vertres01/conf/uk10k_gatk_20120914.filter
##samtoolsVersion=0.1.17 (r973:277)




1 970561 . GGTG GG 190.30 iGQual;iMinQ AC1=1;AC=2;AF1=0.4969;AF=0.50;AN=4;BaseQRankSum=3.668;CSQ=ENST00000379370:AGRN:INTRONIC+ENST00000469403:AGRN:WITHIN_NON_CODING_GENE+ENST00000477585:AGRN:WITHIN_NON_CODING_GENE,INTRONIC;DP4=11,0,4,1;DP=69;FQ=-15.7;FS=0.000;HRun=0;HWE=1.000000;HaplotypeScore=215.7312;ICF=-1.00000;INDEL;MQ0=0;MQ=49;MQRankSum=-0.014;PV4=0.31,1,0.045,1;QD=9.28;ReadPosRankSum=3.724;SB=-1.21;SF=0f,1;TYPE=del GT:GQP:SP:AD:PL 0/1:3:16:0:.:19,0,39 0/1:99:41:.:31,10:.,.,303

1 970562 . GT G 164.07 iGQual;iMinQ AC1=1;AC=2;AF1=0.498;AF=0.50;AN=4;BaseQRankSum=4.767;CSQ=ENST00000379370:AGRN:INTRONIC+ENST00000469403:AGRN:WITHIN_NON_CODING_GENE+ENST00000477585:AGRN:WITHIN_NON_CODING_GENE,INTRONIC;DP4=13,1,3,0;DP=61;FQ=-13.7;FS=0.000;HRun=1;HWE=1.000000;HaplotypeScore=229.9952;ICF=-1.00000;INDEL;MQ0=0;MQ=49.47;MQRankSum=-3.438;PV4=1,0.17,1,1;QD=9.65;ReadPosRankSum=4.349;SB=-27.36;SF=0,1f;TYPE=del GT:GQP:SP:PL:AD 0/1:99:34:.:367,0,323:25,9 0/1:6:17:0:21,0,143

this two row just are continuous position,it seems we could drop 970562
they are all 0/1 0/1

can anyone help me to know about this question ,thx
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