How to get gvcf

On docker or singularity

#To get SNV gvcf using docker
docker run -it -v {inputdir}:/opt/input -v {outputdir}:/opt/outdir -v {refseqdir}:/opt/refdir chuhongyuan/summer conda run -n clair3 /opt/conda/envs/clair3/bin/run_clair3.sh --bam_fn=/opt/input/${sampleID}_alignment.sorted.bam --ref_fn=/opt/refdir/{refseq.fa} -t {number_of_thread} --platform=ont --model_path=/opt/conda/envs/clair3/bin/models/ont(OR r941_prom_sup_g5014) --output=/opt/outdir --gvcf
#To get SV gvcf using docker
docker run -it -v {inputdir}:/opt/input -v {outputdir}:/opt/outdir -v {refseqdir}:/opt/refdir chuhongyuan/summer conda run -n sniffles sniffles --threads {number of thread} --input /opt/input/sample_alignment.sorted.bam --vcf /opt/outdir/sample_sniffles2.vcf --reference /opt/refdir/{refseq.fa}
docker run -it -v {inputdir}:/opt/input -v {outputdir}:/opt/outdir -v {refseqdir}:/opt/refdir chuhongyuan/summer conda run -n sniffles sniffles --threads {number of thread} --input /opt/input/${sampleID}_alignment.sorted.bam --snf /opt/outdir/${sampleID}_output_sorted.snf
docker run -it -v {inputdir}:/opt/input -v {outputdir}:/opt/outdir -v {refseqdir}:/opt/refdir chuhongyuan/summer conda run -n sniffles sniffles --threads {number of thread} --snf /opt/outdir/${sampleID}_output_sorted.snf --vcf /opt/outdir/multisample_sniffles2.vcf


#To get SNV gvcf using singularity
singularity run {summersifdir}/summer.sif conda run -n clair3 /opt/conda/envs/clair3/bin/run_clair3.sh --bam_fn={inputdir}/${sampleID}_alignment_sorted.bam --ref_fn={refdir/refseq} -t {number of thread} --platform=ont --model_path=/opt/conda/envs/clair3/bin/models/ont(OR r941_prom_sup_g5014) --output={outdir} --gvcf
#To get SV gvcf using singularity
singularity run {summersifdir}/summer.sif conda run -n sniffles sniffles --threads {number of thread} --input {inputdir}/input_sorted.bam --vcf {outdir}/sample_sniffles2.vcf --reference {refdir}/refseq.fa
singularity run {summersifdir}/summer.sif conda run -n sniffles sniffles --threads {number of thread} --input {inputdir}/${sampleID}_input_sorted.bam --snf {outputdir}/${sampleID}_output_sorted.snf
singularity run {summersifdir}/summer.sif conda run -n sniffles sniffles --threads {number of thread} --snf {outputdir}/${sampleID}_output_sorted.snf --vcf {outputdir}/multisample_sniffles2.vcf