NGS Shell Script 第五步驟 執行結果請益 #4
Bottlemandy
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我今晚點確認後回覆,謝謝 |
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曼殊妳好, 這個狀況應該與俐斐同學一樣
把下面的參數加到 script 裡面就可以
$GATK4 --java-options "-Xmx4g -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -Djava.io.tmpdir=$TMP_DIR" \
HaplotypeCaller \
-R $REF_HG38_FASTA_1 \
-I $OUTPUT_DIR/${PREFIX}_sorted_rmdup.bam \
--dbsnp $DBSNP_HG38 \
-stand-call-conf 50.0 \
-ERC GVCF \
-O $OUTPUT_DIR/${PREFIX}_allsites.g.vcf.gz |
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林玉祥老師您好:
我是DIGI的學員曼殊,我在執行5_gatk_GVCF_SLURM_job後,不確定執行結果是否正確?想詢問老師是否方便提供正確執行結果供對照?
附上執行結果
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