| bedtools |
2.25.0 |
singularity exec --cleanenv *.sif bedtools |
| bwa |
0.7.17-r1188 |
singularity exec --cleanenv *.sif bwa |
| fastQValidator |
0.1.1a |
singularity exec --cleanenv *.sif fastQValidator |
| fastqc |
0.11.8 |
singularity exec --cleanenv *.sif fastqc |
| sentieon |
2019.11 |
singularity exec --cleanenv *.sif sentieon |
| sentieon_bwa |
2019.11 |
singularity exec --cleanenv *.sif sentieon_bwa |
| qualimap |
2.2.1 |
singularity exec --cleanenv *.sif qualimap |
| bamUtil |
1.0.14 |
singularity exec --cleanenv *.sif bam |
| trimmomatic |
0.39 |
singularity exec --cleanenv *.sif java -jar /home/bmap/software/trimmomatic/Trimmomatic-0.39/trimmomatic.jar |
| samtools |
2.2.1 |
singularity exec --cleanenv *.sif samtools |
| bedmap |
2.4.36(typical) |
singularity exec --cleanenv *.sif bedmap |
| bamtools |
2.5.1 |
singularity exec --cleanenv *.sif bamtools |
| pindel |
0.2.5b9 |
singularity exec --cleanenv *.sif pindel |
| sam2pindel |
0.2.5b9 |
singularity exec --cleanenv *.sif sam2pindel |
| pindel2vcf |
0.2.5b9 |
singularity exec --cleanenv *.sif pindel2vcf |
| annovar |
2018-04-16 |
singularity exec --cleanenv *.sif table_annovar.pl |
| java |
SE 1.8.0_221 |
singularity exec --cleanenv *.sif java |
| GATK |
4.1.2.0 |
singularity --cleanenv exec *.sif gatk |
| SnpEff |
4.3t |
singularity exec --cleanenv *.sif java -jar /home/bmap/software/snpeff/snpEff/snpEff.jar |
| SnpSift |
4.3t |
singularity exec --cleanenv *.sif java -jar /home/bmap/software/snpeff/snpEff/SnpSift.jar |
| picard |
v2.20.4 |
singularity exec --cleanenv *.sif java -jar /home/bmap/software/picard/picard.jar |
| python |
3.5.2 |
singularity exec --cleanenv *.sif python |
| R |
3.6.2 |
singularity exec --cleanenv *.sif R |
Address: 800 Dong Chuan RD. Minhang District, Shanghai, China SJTU-Yale Joint Center for Biostatistics, SJTU