Update README.md

schedule/README.md

@@ -16,8 +16,8 @@ A trio from the [Genome in a Bottle consortium (GIAB)](https://github.com/genome
 | Hands-on | [Evaluating Read Quality with `FastQC`](https://hbctraining.github.io/variant_analysis/lessons/02_fastqc.html) | Reuse with replacement of dataset | Understanding QC of sequence reads |
 | Hands-on | [Sequence Read Alignment](https://hbctraining.github.io/variant_analysis/lessons/03_sequence_alignment_theory.html) | Reuse with replacement of dataset | Alignmnet with bwa, theory and alignment file format |
 | Hands-on | [Alignment File Processing ](https://hbctraining.github.io/variant_analysis/lessons/04_alignment_file_processing.html) | Reuse with replacement of dataset | Mark and remove duplicates, sort BAM file |
-| Hands-on | [Alignment File Quality Control](https://hbctraining.github.io/variant_analysis/lessons/05_alignment_QC.html) | Reuse with replacement of dataset |  |
-| Hands-on | [Aggregating QC metrics using MultiQC](https://hbctraining.github.io/variant_analysis/lessons/06_aggregate_multiqc.html) | Reuse with replacement of dataset - this can be run later and include GATK and Snpeff results in the report (Qualimap; but might only be for WGS) |  |
+| Hands-on | [Alignment File Quality Control](https://hbctraining.github.io/variant_analysis/lessons/05_alignment_QC.html) | Reuse with replacement of dataset (merge with Alignment file processing lesson) | Run Picard CollectAlignmentSummaryMetrics |
+| Hands-on | [Aggregating QC metrics using MultiQC](https://hbctraining.github.io/variant_analysis/lessons/06_aggregate_multiqc.html) | Reuse with replacement of dataset  | This can be run later and include GATK and Snpeff results as input. (Qualimap; but might only be for WGS but worth mentioning) |
 | Hands-on | Variant Calling | New lesson | remove PON / germline resource / MuTect explanation / MuTect code - Add Haplotype caller explanation and code |
 | Hands-on | Variant Annotation | New lesson | remove cancer mode, add annotations from ClinVar, OMIM, dbNSFP (contains many predictive scores as well as ExAC/gnomAD population frequencies)  |
 | Hands-on | Variant Prioritization| New lesson | add filters for population frequency (rare), score annotations (damaging), ClinVar pathogenicity, prioritize two hits in the same gene (for suspected recessive disease), prioritize variants found in proband but not parents (for suspected de novo disease) |