view: 查看 SAM/BAM 文件的内容,可以指定输出格式和过滤条件,也可以查看参考序列的信息。 merge: 合并多个 BAM 文件,可以自动处理 header 和压缩级别。 flagstat: 统计 BAM 文件中的 reads 的标志位,可以显示 QC 通过和失败的 reads 数目,以及各种配对情况和重复情况。 markdup: 标记或者移除 BAM 文件中的重复 r...
view: 查看 SAM/BAM 文件的内容,可以指定输出格式和过滤条件,也可以查看参考序列的信息。 merge: 合并多个 BAM 文件,可以自动处理 header 和压缩级别。 flagstat: 统计 BAM 文件中的 reads 的标志位,可以显示 QC 通过和失败的 reads 数目,以及各种配对情况和重复情况。 markdup: 标记或者移除 BAM 文件中的重复 r...
So it's trying to open up more files than are allowed for one process. I'm manually merging the tmp files in chunks, so a simple solution would be to simply check this limit and do the merge in chunks into tmp files that are then later merged if the number of files is too high. ...
Trying to run with -m too small can lead to the creation of a very large number of temporary files. This may make sort fail due to it exceeding limits on the number of files it can have open at the same time. I could have stated the error message I received from samtools: ...
I have compiled a curious test case for bcftools merge: samples.tar.gz This contains vcf.gz files and respective indices for four samples. sample1 contains only the header and no records. sample2 and sample4 contain the same alternative ...
Could you go to the work directory of the merge_transcriptomes and if its small enough perhaps zip up and send the final_non_redundant_transcriptome.fasta and if possible also the gtf file from that directory? Just to check it looks sensible?Author...
bcftools merge: Update headers when appropriate with the '--info-rules *:join' INFO rule. (#1282) Local alleles merging that produce LAA and LPL when requested, a draft implementation of samtools/hts-specs#434 (#1138) New --no-index which allows to merge unindexed files. Requires the in...
The problem is probably too many open files — see e.g.#329and#1022. We had a go at producing a better error message for this case back in 2015 (seesamtools/htslib#288), but that particular PR wasn't a good solution to the problem, as noted in the mailing list conversation of the...
Hello, I have 3 vcf.gz files A, B and C that I want to merge with bcftools. Each file was generated by: Concatenating each individual chromosome vcf.gz file using concat Uncompressed with mv Compressed with bgzip Indexed with tabix After...
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