SNP analysis

How to find SNPs

mpileup file:

TranscriptID    position        base@position   actual_reads_and_qual
E2F4|ENSG00000205250|c.XGI_TC419474|JGIv7b.000015416_1879975-1902638-   15      A       1

$ samtools mpileup overexpression_expt.my.sorted.bam > overexpression_expt.my.sorted.mpileup

E2F4|ENSG00000205250|c.XGI_TC419474|JGIv7b.000015416_1879975-1902638-   15      N       1
E2F4|ENSG00000205250|c.XGI_TC419474|JGIv7b.000015416_1879975-1902638-   16      N       0
E2F4|ENSG00000205250|c.XGI_TC419474|JGIv7b.000015416_1879975-1902638-   17      N       1
E2F4|ENSG00000205250|c.XGI_TC419474|JGIv7b.000015416_1879975-1902638-   18      N       0
E2F4|ENSG00000205250|c.XGI_TC419474|JGIv7b.000015416_1879975-1902638-   19      N       2

$ samtools mpileup -f Baby_laevis_models.fasta overexpression_expt.my.sorted.bam > overexpression_expt.my.sorted.mpileup

E2F4|ENSG00000205250|c.XGI_TC419474|JGIv7b.000015416_1879975-1902638-   15      C       1
E2F4|ENSG00000205250|c.XGI_TC419474|JGIv7b.000015416_1879975-1902638-   16      A       0
E2F4|ENSG00000205250|c.XGI_TC419474|JGIv7b.000015416_1879975-1902638-   17      G       1
E2F4|ENSG00000205250|c.XGI_TC419474|JGIv7b.000015416_1879975-1902638-   18      T       0
E2F4|ENSG00000205250|c.XGI_TC419474|JGIv7b.000015416_1879975-1902638-   19      G       2

$ java -jar VarScan.v2.3.6.jar mpileup2snp overexpression_expt.my.sorted.mpileup  > overexpression_expt.snps

FOXI1|ENSG00000168269|c.Quigley201207_X000481|JGIv7b.000003467_436433-439641+   99      C       T       Y:33:19:14:42.42%:1.0577E-5     Pass:1.0:19:0:14:0:1E0  0       1       0       0       Y:33:19:14:4
2.42%:1.0577E-5
FOXI1|ENSG00000168269|c.Quigley201207_X000481|JGIv7b.000003467_436433-439641+   156     T       C       C:28:7:21:75%:8.7917E-10        Pass:1.0:7:0:21:0:1E0   0       0       1       0       C:28:7:21:75
%:8.7917E-10
FOXI1|ENSG00000168269|c.Quigley201207_X000481|JGIv7b.000003467_436433-439641+   222     G       T       K:42:32:10:23.81%:5.3293E-4     Pass:1.0:32:0:10:0:1E0  0       1       0       0       K:42:32:10:2
3.81%:5.3293E-4

$ java -jar VarScan.v2.3.6.jar mpileup2snp overexpression_expt.my.sorted.mpileup --output-vcf > overexpression_expt.vcf

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  Sample1
E2F4|ENSG00000205250|c.XGI_TC419474|JGIv7b.000015416_1879975-1902638-   2047    .       G       A       PASS    ADP=40;WT=0;HET=1;HOM=0;NC=0    GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR
        0/1:113:41:40:11:27:67.5%:4.2271E-12:35:33:11:0:27:0
FOXI1|ENSG00000168269|c.Quigley201207_X000286|JGIv7b.000001168_1510409-1513739- 825     .       T       PASS    ADP=27;WT=0;HET=1;HOM=0;NC=0    GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR
:ADF:ADR        0/1:38:27:27:16:11:40.74%:1.362E-4:36:32:16:0:11:0

Galaxy session

https://usegalaxy.org/u/savova/h/xenopusworkshop