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Archivos de entrada Genoma Paciente: hg38.fa.gz Lecturas: SRR1517848_1.fastq.gz SRR1517848_2.fastq.gz

sudo apt install tabix sudo apt install pv pv hg38.fa | bgzip -@ 8 > hg38.fa.gz sudo apt install vmtouch samtools faidx hg38.fa.gz chr1:1-60

git clone --depth 1 https://github.com/ksahlin/strobealign.git mkdir build cd build

sudo apt install libisal-dev cmake .. -DCMAKE_BUILD_TYPE=Release make -j$(nproc) sudo make install

strobealign -t 8 --use-index -r 150
datasets/reference_genome/hg38.fa.gz
datasets/fastq/SRR1517848_1.fastq.gz
datasets/fastq/SRR1517848_2.fastq.gz
| samtools sort -o datasets/bam/SRR1517848_aligned.bam

BAM a CRAM

samtools view -T datasets/reference_genome/hg38.fa.gz
-C -o datasets/bam/SRR1517848_aligned.cram
datasets/bam/SRR1517848_aligned.bam

indexar el CRAM

samtools index datasets/bam/SRR1517848_aligned.cram rm datasets/bam/sample_sorted.bam

Generar mpileup con bcftools y llamar variantes

bcftools mpileup -f datasets/reference_genome/hg38.fa.gz
-Ou
datasets/bam/SRR1517848_aligned.cram |
bcftools call -mv -Ob -o datasets/bam/SRR1517848_variants.bcf

bcftools view datasets/bam/SRR1517848_variants.bcf -Ov -o datasets/bam/SRR1517848_variants.vcf

He realizados las pruebas en consola, para el test.

Me ha funcionado esto

Archivos de entrada Genoma Paciente: hg38.fa.gz Lecturas: SRR1517848_1.fastq.gz SRR1517848_2.fastq.gz

sudo apt install tabix sudo apt install pv pv hg38.fa | bgzip -@ 8 > hg38.fa.gz sudo apt install vmtouch samtools faidx hg38.fa.gz chr1:1-60

git clone --depth 1 https://github.com/ksahlin/strobealign.git mkdir build cd build

sudo apt install libisal-dev cmake .. -DCMAKE_BUILD_TYPE=Release make -j$(nproc) sudo make install

strobealign -t 8 --use-index -r 150
datasets/reference_genome/hg38.fa.gz
datasets/fastq/SRR1517848_1.fastq.gz
datasets/fastq/SRR1517848_2.fastq.gz
| samtools sort -o datasets/bam/SRR1517848_aligned.bam

BAM a CRAM

samtools view -T datasets/reference_genome/hg38.fa.gz
-C -o datasets/bam/SRR1517848_aligned.cram
datasets/bam/SRR1517848_aligned.bam

indexar el CRAM

samtools index datasets/bam/SRR1517848_aligned.cram rm datasets/bam/sample_sorted.bam

Generar mpileup con bcftools y llamar variantes

bcftools mpileup -f datasets/reference_genome/hg38.fa.gz
-Ou
datasets/bam/SRR1517848_aligned.cram |
bcftools call -mv -Ob -o datasets/bam/SRR1517848_variants.bcf

bcftools view datasets/bam/SRR1517848_variants.bcf -Ov -o datasets/vcf/SRR1517848_variants.vcf

Comprueba que en los contenedores docker donde se ejecutan estas pruebas, tenemos lo necesario para ejecutarlas.

Tambień revisa que las pipelines tienen lo necesario para ejecurarse

./dev.sh start