Hi all,
I visualized the variant positions I got from varScan using IGV.
I saw that they show different coverage from what I have detected using varScan (usually the IGV have higher coverage for both variant and reference).
i also use -B in mpileup or --min-avg-qual 0 in varscan ( although my quality 's so good ~ 30 -> 40 phred score), but IGV alway have more read than IGV
Example
IGV
total count :235396
A:363(0%,213+,150-)
B:82094(44771+,37323-)
C:144(80+,64-)
D:152795(82683,+70112-)
N:0
Varscan
chr9 133738357 rs121913461 T C . PASS ADP=7996;WT=0;HET=1;HOM=0;NC=0;GENEINFO=ABL1:25;LSD=true;NSM=true;OM=true;OTHERKG=true;PM=true;REF=true;RS=121913461;RSPOS=133738357;S3D=true;SAO=3;SSR=0;VC=SNV;VP=0x050260000a01000002110120;WGT=1;dbSNPBuildID=133;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y253H|1130|ABL1||CODING|NM_005157.4|4|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y272H|1149|ABL1||CODING|NM_007313.2|4|1) GT:GQ:SDPP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:255:7996:7996:5248:2736:34.22%:0E0:35:36:4528:720:2343:393
-> i see DP is very smaller than IGV
i also read dkoboldt's blog about 5 things of mpileup
Thank in advance.
I visualized the variant positions I got from varScan using IGV.
I saw that they show different coverage from what I have detected using varScan (usually the IGV have higher coverage for both variant and reference).
i also use -B in mpileup or --min-avg-qual 0 in varscan ( although my quality 's so good ~ 30 -> 40 phred score), but IGV alway have more read than IGV
Example
IGV
total count :235396
A:363(0%,213+,150-)
B:82094(44771+,37323-)
C:144(80+,64-)
D:152795(82683,+70112-)
N:0
Varscan
chr9 133738357 rs121913461 T C . PASS ADP=7996;WT=0;HET=1;HOM=0;NC=0;GENEINFO=ABL1:25;LSD=true;NSM=true;OM=true;OTHERKG=true;PM=true;REF=true;RS=121913461;RSPOS=133738357;S3D=true;SAO=3;SSR=0;VC=SNV;VP=0x050260000a01000002110120;WGT=1;dbSNPBuildID=133;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y253H|1130|ABL1||CODING|NM_005157.4|4|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y272H|1149|ABL1||CODING|NM_007313.2|4|1) GT:GQ:SDPP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:255:7996:7996:5248:2736:34.22%:0E0:35:36:4528:720:2343:393
-> i see DP is very smaller than IGV
i also read dkoboldt's blog about 5 things of mpileup
Thank in advance.
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