Hi Everyone, after surpass all the inconvenients of installation in an IMac I've finally capable to perform several steps following the GATK pipeline runing it directly in the terminal
for Illumina Data
this are the steps completed:
1. Concatenate the HG19
2. INdex the HG19 with BWA
3. Align the FASTQ sequences to the genome using BWA mem
4. Sort the .sam file to create the .bam with Picard
5. Mark duplicates with picard too
6. add the RG with picard
But I have a huge question... how I do know that my analysis is good? that my BWA are correctly aligned, that the sort and duplicates are correctly marked and the BAM file is good. exist a way to know that?
thanks a lot for your time.
Regards
Camilo Andres
Biological Engineer
for Illumina Data
this are the steps completed:
1. Concatenate the HG19
2. INdex the HG19 with BWA
3. Align the FASTQ sequences to the genome using BWA mem
4. Sort the .sam file to create the .bam with Picard
5. Mark duplicates with picard too
6. add the RG with picard
But I have a huge question... how I do know that my analysis is good? that my BWA are correctly aligned, that the sort and duplicates are correctly marked and the BAM file is good. exist a way to know that?
thanks a lot for your time.
Regards
Camilo Andres
Biological Engineer
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