data內應該有哪些檔案? #5
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jameschiu1023
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我今晚點回覆,謝謝 |
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你好, 第五步驟的問題你可以檢查你的 log 裡面寫了什麼線索,從問題中再做推敲 有兩個同學(俐斐,曼殊)也問相同的問題, 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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老師好,
今天操作到第5個步驟後就無法順利進行,所以想請教您是否在自己的data裡面需要有以下這個檔案:「Homo_sapiens_assembly38.dbsnp138.vcf」
因為我看到好幾個script都有需要用到這個檔案但是我自己的data卻沒有,所以想請教您。
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