Is STAR Wasp compatible with STAR solo?

[leakiefer]

Hi Alex,

I am trying to analyze allele-specific single cell RNAseq data collected through 10x chromium v2 and I was wondering if Wasp allele specific calling would work in the context of STAR solo. And if yes would it be as simple as adding --waspOutputMode SAMtag and --varVCFfile file.vcf as a tag to the suggested STAR solo tags?

Thank you!

[alexdobin]

Hi Lea,

yes, --waspOutputMode SAMtag and --varVCFfile file.vcf will work with STARsolo options and will output vW tags in the BAM file.

Cheers Alex

[xiaohe0404]

Hi Alex, I used wasp with STARsolo, however there was no vM tag in output Bam at all. I really wanna know why.

Here is my code below: my STAR version is 2.7.8a

STAR --genomeDir STARsolo/STAR_refindex --soloType CB_UMI_Simple --soloFeatures Gene SJ --readFilesIn 682_683.deDup.bam --readFilesType SAM SE --readFilesCommand samtools view -F 0x100 --outSAMattributes GX GN sS sQ sM vA vG vW --outSAMtype BAM Unsorted --soloInputSAMattrBarcodeSeq CR UR --soloInputSAMattrBarcodeQual CY UY --runThreadN 20 --soloCBwhitelist None --outFileNamePrefix ./682_683_vM/682_683 --outSAMunmapped Within --waspOutputMode SAMtag --varVCFfile 682_683.vcf

Here is my Input Bam file below:

SRR18028384.37324214    16      chr1    14459   0       98M     *       0       0       AACACAGTGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGAGCACAGGCAGACAGAAGTCCCCACCCCAGCTGTGTGGCCTCAGGCCAGCCTTCCGCT      FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF      NH:i:5  HI:i:1  AS:i:92 nM:i:2  RE:A:I  xf:i:0  CR:Z:CACCACTAGCCGGTAA   CY:Z:FFFFFFFFFFFFFFFF   CB:Z:CACCACTAGCCGGTAA-1 UR:Z:AGGACTGTTG UY:Z:FFFFFFFFFF UB:Z:AGGACTGTTG RG:Z:pool1:0:1:unknow_flowcell:0
SRR18028383.3589711     16      chr1    14459   0       98M     *       0       0       AACACAGTGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGAGCACAGGCAGACAGAAGTCCCCACCCCAGCTGTGTGGCCTCAGGCCAGCCTTCCGCT      FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF      NH:i:5  HI:i:1  AS:i:92 nM:i:2  RE:A:I  xf:i:0  CR:Z:CACCACTAGCCGGTAA   CY:Z:FFFFFFFFFFFFFFFF   CB:Z:CACCACTAGCCGGTAA-1 UR:Z:AGGACTGTTG UY:Z:FFFFFFFFFF UB:Z:AGGACTGTTG RG:Z:pool1:0:1:unknow_flowcell:0

And here is my vcf file :

chr1    794299  1:729679     C  G       .       PASS    AF=0.84121;MAF=0.15879;R2=0.85066   GT  1|1
chr1    796338  1:731718     T  C       .       PASS    AF=0.11641;MAF=0.11641;R2=0.8173    GT  0|0
chr1    798969  1:734349     T  C       .       PASS    AF=0.1153;MAF=0.1153;R2=0.82868 GT  0|0
chr1    800909  1:736289     T  A       .       PASS    AF=0.12816;MAF=0.12816;R2=0.84779   GT  0|0
chr1    817186  1:752566     G  A       .       PASS    AF=0.84074;MAF=0.15926;R2=0.99139   GT  1|1
chr1    817341  1:752721     A  G       .       GENOTYPED;PASS  AF=0.83896;ER2=0.85157;MAF=0.16104;R2=0.99875   GT      1|1
chr1    818025  1:753405     C  A       .       PASS    AF=0.87744;MAF=0.12256;R2=0.94849   GT  1|1
chr1    818161  1:753541     G  A       .       PASS    AF=0.12352;MAF=0.12352;R2=0.94906   GT  0|0
chr1    818802  1:754182     A  G       .       PASS    AF=0.87603;MAF=0.12397;R2=0.95195   GT  1|1
chr1    818812  1:754192     A  G       .       PASS    AF=0.87606;MAF=0.12394;R2=0.95203   GT  1|1

I would really appreciate it if you could give me some suggestion! Best wishes!

[alexdobin]

Hi @xiaohe0404

vG/vW tags will appear only for reads that overlap variants.

[alexdobin]

Hi @xiaohe0404

vG/vW tags will appear only for reads that overlap variants.